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The 'OmicFlow' requires an up-front validated metadata template from the user, which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. Once this unified structure is established, users can perform manual subsetting, visualization, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.", "homepage": "https://github.com/agusinac/OmicFlow", "biotoolsID": "omicflow", "biotoolsCURIE": "biotools:omicflow", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/agusinac/OmicFlow/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow", "type": [ "Repository" ], "note": null }, { "url": "https://cran.r-project.org/package=OmicFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/OmicFlow/OmicFlow.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/agusinac/OmicFlow/blob/main/README.md", "type": [ "General" ], "note": "Metadata File Instructions" } ], "publication": [], "credit": [], "owner": "agusinac", "additionDate": "2025-08-20T09:24:38.732312Z", "lastUpdate": "2025-09-02T06:28:57.092837Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinProspector", "description": "A suite of protein identification tools.", "homepage": "http://prospector.ucsf.edu", "biotoolsID": "proteinprospector", "biotoolsCURIE": "biotools:proteinprospector", "version": [], "otherID": [ { "value": "RRID:SCR_014558", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3647", "term": "Blind peptide database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3489", "term": "Database management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://prospector.ucsf.edu/prospector/html/instruct/allman.htm", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1074/mcp.d500002-mcp200", "pmid": "15937296", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cells, time-of-flight mass spectrometer: II New developments in protein prospector allow for reliable and comprehensive automatic analysis of large datasets", "abstract": "A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine \"Mascot\" using a new results comparison program within Prospector named \"SearchCompare.\" The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.", "date": "2005-08-01T00:00:00Z", "citationCount": 165, "authors": [ { "name": "Chalkley R.J." }, { "name": "Baker P.R." }, { "name": "Huang L." }, { "name": "Hansen K.C." }, { "name": "Allen N.P." }, { "name": "Rexach M." }, { "name": "Burlingame A.L." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Admin", "email": "ppadmin@cgl.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:18Z", "lastUpdate": "2025-08-28T15:15:11.245617Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Make2D-DB II", "description": "Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web.", "homepage": "https://world-2dpage.expasy.org/make2ddb/", "biotoolsID": "make2d-db_ii", "biotoolsCURIE": "biotools:make2d-db_ii", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://world-2dpage.expasy.org/make2ddb/1.Readme_main.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:40Z", "lastUpdate": "2025-08-28T13:43:51.088758Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Swiss Mass Abacus", "description": "Calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.", "homepage": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "biotoolsID": "swiss_mass_abacus", "biotoolsCURIE": "biotools:swiss_mass_abacus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0122", "term": "Structural genomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/swiss-mass-abacus/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:54Z", "lastUpdate": "2025-08-28T13:43:28.119620Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Glydin", "description": "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.", "homepage": "https://glycoproteome.expasy.org/epitopes/", "biotoolsID": "glydin", "biotoolsCURIE": "biotools:glydin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://glycoproteome.expasy.org/epitopes/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-12-06T18:14:30Z", "lastUpdate": "2025-08-28T13:41:40.603256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MaCPepDB - Mass Centric Peptide Database", "description": "A Database to Quickly Access All Tryptic Peptides of the UniProtKB", "homepage": "https://macpepdb.cubimed.rub.de/", "biotoolsID": "macpepdb_-_mass_centric_peptide_database", "biotoolsCURIE": "biotools:macpepdb_-_mass_centric_peptide_database", "version": [ "3.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "Rust", "JavaScript", "Other" ], "license": null, "collectionID": [ "CUBiMed.RUB", "BioInfra.Prot" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/medbioinf/macpepdb", "type": [ "Repository" ], "note": "Backend implementation written in Rust / Axum" }, { "url": "https://github.com/medbioinf/macpepdb-frontend", "type": [ "Repository" ], "note": "Frontend implementation written in Rust / Dioxus" } ], "download": [], "documentation": [ { "url": "https://docs.rs/macpepdb/latest/macpepdb/web/index.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.0c00967", "pmid": "33724838", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKB", "abstract": "Protein sequence databases play a crucial role in the majority of the currently applied mass-spectrometry-based proteomics workflows. Here UniProtKB serves as one of the major sources, as it combines the information of several smaller databases and enriches the entries with additional biological information. For the identification of peptides in a sample by tandem mass spectra, as generated by data-dependent acquisition, protein sequence databases provide the basis for most spectrum identification search engines. In addition, for targeted proteomics approaches like selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), knowledge of the peptide sequences, their masses, and whether they are unique for a protein is essential. Because most bottom-up proteomics approaches use trypsin to cleave the proteins in a sample, the tryptic peptides contained in a protein database are of great interest. We present a database, called MaCPepDB (mass-centric peptide database), that consists of the complete tryptic digest of the Swiss-Prot and TrEMBL parts of UniProtKB. This database is especially designed to not only allow queries of peptide sequences and return the respective information about connected proteins and thus whether a peptide is unique but also allow queries of specific masses of peptides or precursors of MS/MS spectra. Furthermore, posttranslational modifications can be considered in a query as well as different mass deviations for posttranslational modifications. Hence the database can be used by a sequence query not only to, for example, check in which proteins of the UniProt database a tryptic peptide can be found but also to find possibly interfering peptides in PRM/SRM experiments using the mass query. The complete database contains currently 5 939 244 990 peptides from 185 561 610 proteins (UniProt version 2020_03), for which a single query usually takes less than 1 s. For easy exploration of the data, a web interface was developed. A REST application programming interface (API) for programmatic and workflow access is also available at https://macpepdb.mpc.rub.de.", "date": "2021-04-02T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Uszkoreit J." }, { "name": "Winkelhardt D." }, { "name": "Barkovits K." }, { "name": "Wulf M." }, { "name": "Roocke S." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Dirk Winkelhardt", "email": "dirk.winkelhardt@rub.de", "url": null, "orcidid": "https://orcid.org/0000-0001-8770-2221", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "PD Dr. Martin Eisenacher", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2687-7444", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "di_hardt", "additionDate": "2023-07-25T12:35:27.605861Z", "lastUpdate": "2025-07-31T09:03:29.192901Z", "editPermission": { "type": "group", "authors": [ "di_hardt", "julianu", "BioInfra.Prot" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OakMine", "description": "Quercus robur annotation database", "homepage": "https://urgi.versailles.inra.fr/OakMine_PM1N", "biotoolsID": "OakMine", "biotoolsCURIE": "biotools:OakMine", "version": [ "2.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3753", "term": "Over-representation data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3786", "term": "Query script" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Ruby", "Java", "Python", "JavaScript", "Perl" ], "license": "LGPL-2.1", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://registry.intermine.org", "type": [ "Software catalogue" ], "note": null }, { "url": "http://intermine.org", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://intermine.readthedocs.org/en/latest/web-services/", "type": [ "API documentation" ], "note": null }, { "url": "https://flymine.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts577", "pmid": "23023984", "pmcid": "PMC3516146", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data", "abstract": "InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. © The Author 2012. Published by Oxford University Press. 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There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.", "date": "2024-11-19T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Klein J." }, { "name": "Lam H." }, { "name": "Mak T.D." }, { "name": "Bittremieux W." }, { "name": "Perez-Riverol Y." }, { "name": "Gabriels R." }, { "name": "Shofstahl J." }, { "name": "Hecht H." }, { "name": "Binz P.-A." }, { "name": "Kawano S." }, { "name": "Van Den Bossche T." }, { "name": "Carver J." }, { "name": "Neely B.A." }, { "name": "Mendoza L." }, { "name": "Suomi T." }, { "name": "Claeys T." }, { "name": "Payne T." }, { "name": "Schulte D." }, { "name": "Sun Z." }, { "name": "Hoffmann N." }, { "name": "Zhu Y." }, { "name": "Neumann S." }, { "name": "Jones A.R." }, { "name": "Bandeira N." }, { "name": "Vizcaino J.A." }, { "name": "Deutsch E.W." } ], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "recetox-specdatri", "additionDate": "2025-06-12T11:47:48.641345Z", "lastUpdate": "2025-06-12T11:57:26.484553Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PeptideProphet", "description": "Validation of peptide identifications by MS/MS and database searches.", "homepage": "http://peptideprophet.sourceforge.net/index.html", "biotoolsID": "peptideprophet", "biotoolsCURIE": "biotools:peptideprophet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3675", "term": "Variant filtering" }, { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++", "Perl" ], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null }, { "url": "http://tools.proteomecenter.org/PeptideProphet.php", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/peptideprophet/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideProphet", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ac025747h", "pmid": "12403597", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search", "abstract": "We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic termini of peptides. Using SEQUEST search results for spectra generated from a sample of known protein components, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared.", "date": "2002-10-15T00:00:00Z", "citationCount": 4142, "authors": [ { "name": "Keller A." }, { "name": "Nesvizhskii A.I." }, { "name": "Kolker E." }, { "name": "Aebersold R." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "nesvi@umich.edu", "email": "nesvi@umich.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "akeller@systemsbiology.org", "email": "akeller@systemsbiology.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:29Z", "lastUpdate": "2025-06-11T07:30:21.805189Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinProphet", "description": "Validation of protein identifications by MS/MS and database searches.", "homepage": "http://tools.proteomecenter.org/ProteinProphet.php", "biotoolsID": "proteinprophet", "biotoolsCURIE": "biotools:proteinprophet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3648", "term": "Validation of peptide-spectrum matches" }, { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" }, { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Perl", "C" ], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/proteinprophet/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "14632076", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A statistical model for identifying proteins by tandem mass spectrometry", "abstract": "A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample. Peptides that correspond to more than a single protein in the sequence database are apportioned among all corresponding proteins, and a minimal protein list sufficient to account for the observed peptide assignments is derived using the expectation-maximization algorithm. Using peptide assignments to spectra generated from a sample of 18 purified proteins, as well as complex H. influenzae and Halobacterium samples, the model is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications. This method allows filtering of large-scale proteomics data sets with predictable sensitivity and false positive identification error rates. Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments.", "date": "2003-09-01T00:00:00Z", "citationCount": 3996, "authors": [ { "name": "Nesvizhskii A.I." }, { "name": "Keller A." }, { "name": "Kolker E." }, { "name": "Aebersold R." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "nesvi@umich.edu", "email": "nesvi@umich.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:30Z", "lastUpdate": "2025-06-11T07:29:44.805939Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MSI-R", "description": "Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals.\n\nUsing Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data.\n\nThis repository contains the python script performing the recalibration of mass spectrometry images (MSI) from the associated paper Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data.", "homepage": "https://github.com/LaRoccaRaphael/MSI_recalibration", "biotoolsID": "msi-r", "biotoolsCURIE": "biotools:msi-r", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/acs.analchem.0c05071", "pmid": "33583182", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Adaptive pixel mass recalibration for mass spectrometry imaging based on locally endogenous biological signals", "abstract": "Mass spectrometry imaging (MSI) is a powerful and convenient method for revealing the spatial chemical composition of different biological samples. Molecular annotation of the detected signals is only possible if a high mass accuracy is maintained over the entire image and the m/z range. However, the change in the number of ions from pixel-to-pixel of the biological samples could lead to small fluctuations in the detected m/z-values, called mass shift. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. Their “a priori” selection for a global MSI acquisition is prone to false positive detection and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of pixel-specific internal calibrating ions, automatically generated in a data-adaptive manner (https://github.com/ LaRoccaRaphael/MSI_recalibration). Through a practical example, we applied the methodology to a zebrafish whole-body section acquired at a high mass resolution to demonstrate the impact of mass shift on data analysis and the capability of our algorithm to recalibrate MSI data. In addition, we illustrate the broad applicability of the method by recalibrating 31 different public MSI data sets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations (gaining from 20 up to 400 additional annotations), particularly the high-confidence annotations with a low false discovery rate.", "date": "2021-03-02T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Rocca R.L." }, { "name": "Kune C." }, { "name": "Tiquet M." }, { "name": "Stuart L." }, { "name": "Eppe G." }, { "name": "Alexandrov T." }, { "name": "de Pauw E." }, { "name": "Quinton L." } ], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "Niclaskn", "additionDate": "2021-03-19T09:12:19Z", "lastUpdate": "2025-06-05T11:49:34.683716Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MSIWarp", "description": "A General Approach to Mass Alignment in Mass Spectrometry Imaging.\n\nMSIWarp is a flexible tool to perform mass alignment of Mass Spectrometry Imaging (MSI) spectra. A key feature of MSIWarp is its compatibility with centroid spectra.", "homepage": "https://github.com/horvatovichlab/MSIWarp", "biotoolsID": "msiwarp", "biotoolsCURIE": "biotools:msiwarp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [], "language": [ "C++", "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/acs.analchem.0c03833", "pmid": "33317272", "pmcid": "PMC7745203", "type": [], "version": null, "note": null, "metadata": { "title": "MSIWarp: A General Approach to Mass Alignment in Mass Spectrometry Imaging", "abstract": "Mass spectrometry imaging (MSI) is a technique that provides comprehensive molecular information with high spatial resolution from tissue. Today, there is a strong push toward sharing data sets through public repositories in many research fields where MSI is commonly applied; yet, there is no standardized protocol for analyzing these data sets in a reproducible manner. Shifts in the mass-to-charge ratio (m/z) of molecular peaks present a major obstacle that can make it impossible to distinguish one compound from another. Here, we present a label-free m/z alignment approach that is compatible with multiple instrument types and makes no assumptions on the sample's molecular composition. Our approach, MSIWarp (https://github.com/horvatovichlab/MSIWarp), finds an m/z recalibration function by maximizing a similarity score that considers both the intensity and m/z position of peaks matched between two spectra. MSIWarp requires only centroid spectra to find the recalibration function and is thereby readily applicable to almost any MSI data set. To deal with particularly misaligned or peak-sparse spectra, we provide an option to detect and exclude spurious peak matches with a tailored random sample consensus (RANSAC) procedure. We evaluate our approach with four publicly available data sets from both time-of-flight (TOF) and Orbitrap instruments and demonstrate up to 88% improvement in m/z alignment.", "date": "2020-12-15T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Eriksson J.O." }, { "name": "Sanchez Brotons A." }, { "name": "Rezeli M." }, { "name": "Suits F." }, { "name": "Marko-Varga G." }, { "name": "Horvatovich P." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Peter Horvatovich", "email": "p.l.horvatovich@rug.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Niclaskn", "additionDate": "2021-01-18T12:22:18Z", "lastUpdate": "2025-06-05T11:41:35.873717Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "high" }, { "name": "MALDIquant", "description": "MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.", "homepage": "https://cran.r-project.org/package=MALDIquant", "biotoolsID": "maldi_quant", "biotoolsCURIE": "biotools:maldi_quant", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sgibb/MALDIquant/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/sgibb/MALDIquant/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "http://strimmerlab.org/software/maldiquant/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/MALDIquant/MALDIquant.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts447", "pmid": "22796955", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Maldiquant: A versatile R package for the analysis of mass spectrometry data", "abstract": "MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-09-01T00:00:00Z", "citationCount": 499, "authors": [ { "name": "Gibb S." }, { "name": "Strimmer K." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Sebastian Gibb", "email": "mail@sebastiangibb.de", "url": null, "orcidid": "https://orcid.org/0000-0001-7406-4443", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Korbinian Strimmer", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7917-2056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:42:18Z", "lastUpdate": "2025-06-05T11:28:57.497366Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PIA - Protein Inference Algorithms", "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.", "homepage": "https://github.com/medbioinf/pia", "biotoolsID": "pia", "biotoolsCURIE": "biotools:pia", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "knime", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3713", "term": "Mascot .dat file" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3684", "term": "PRIDE XML" }, { "uri": "http://edamontology.org/format_3711", "term": "X!Tandem XML" }, { "uri": "http://edamontology.org/format_3702", "term": "MSF" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] } ], "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "BioInfra.Prot", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/medbioinf/pia", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/pia", "type": "Source code", "note": null, "version": null }, { "url": "http://bioconda.github.io/recipes/pia/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/mpc-bioinformatics/pia/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://hub.docker.com/r/julianusz/pia", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/medbioinf/pia/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.5b00121", "pmid": "25938255", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface", "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.", "date": "2015-07-02T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Uszkoreit J." }, { "name": "Maerkens A." }, { "name": "Perez-Riverol Y." }, { "name": "Meyer H.E." }, { "name": "Marcus K." }, { "name": "Stephan C." }, { "name": "Kohlbacher O." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.8b00723", "pmid": "30474983", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats", "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.", "date": "2019-02-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Uszkoreit J." }, { "name": "Perez-Riverol Y." }, { "name": "Eggers B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": "julian.uszkoreit@rub.de", "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "CUBiMed.RUB", "email": "cubimed@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "julianu", "additionDate": "2016-07-12T10:54:05Z", "lastUpdate": "2025-05-02T13:15:26.717477Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenMS", "description": "Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView.", "homepage": "http://www.openms.de", "biotoolsID": "openms", "biotoolsCURIE": "biotools:openms", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3628", "term": "Chromatographic alignment" }, { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_3633", "term": "Retention time prediction" }, { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_3705", "term": "Isotope-coded protein label" }, { "uri": "http://edamontology.org/operation_3634", "term": "Label-free quantification" }, { "uri": "http://edamontology.org/operation_3639", "term": "iTRAQ" }, { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" }, { "uri": "http://edamontology.org/operation_3635", "term": "Labeled quantification" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" }, { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" }, { "uri": "http://edamontology.org/operation_3023", "term": "Prediction and recognition (protein)" }, { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_3248", "term": "mzQuantML" }, { "uri": "http://edamontology.org/format_3652", "term": "dta" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_2549", "term": "OBO" }, { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": 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All rights reserved.High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.", "date": "2016-08-30T00:00:00Z", "citationCount": 246, "authors": [ { "name": "Rost H.L." }, { "name": "Sachsenberg T." }, { "name": "Aiche S." }, { "name": "Bielow C." }, { "name": "Weisser H." }, { "name": "Aicheler F." }, { "name": "Andreotti S." }, { "name": "Ehrlich H.-C." }, { "name": "Gutenbrunner P." }, { "name": "Kenar E." }, { "name": "Liang X." }, { "name": "Nahnsen S." }, { "name": "Nilse L." }, { "name": "Pfeuffer J." }, { "name": "Rosenberger G." }, { "name": "Rurik M." }, { "name": "Schmitt U." }, { "name": "Veit J." }, { "name": "Walzer M." }, { "name": "Wojnar D." }, { "name": "Wolski W.E." }, { "name": "Schilling O." }, { "name": "Choudhary J.S." }, { "name": "Malmstrom L." }, { "name": "Aebersold R." }, { "name": "Reinert K." }, { "name": "Kohlbacher O." } ], "journal": "Nature Methods" } }, { "doi": "10.1007/978-1-60761-987-1_23", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "OpenMS and TOPP: open source software for LC-MS data analysis.", "abstract": "Proteomics experiments based on state-of-the-art mass spectrometry produce vast amounts of data, which cannot be analyzed manually. Hence, software is needed which is able to analyze the data in an automated fashion. The need for robust and reusable software tools triggered the development of libraries implementing different algorithms for the various analysis steps. OpenMS is such a software library and provides a wealth of data structures and algorithms for the analysis of mass spectrometric data. For users unfamiliar with programming, TOPP (\"The OpenMS Proteomics Pipeline\") offers a wide range of already implemented tools sharing the same interface and designed for a specific analysis task each. TOPP thus makes the sophisticated algorithms of OpenMS accessible to nonprogrammers. The individual TOPP tools can be strung together into pipelines for analyzing mass spectrometry-based experiments starting from the raw output of the mass spectrometer. These analysis pipelines can be constructed using a graphical editor. Even complex analytical workflows can thus be analyzed with ease.", "date": "2011-01-01T00:00:00Z", "citationCount": 65, "authors": [ { "name": "Bertsch A." }, { "name": "Gropl C." }, { "name": "Reinert K." }, { "name": "Kohlbacher O." } ], "journal": "Methods in molecular biology (Clifton, N.J.)" } } ], "credit": [ { "name": "ETH Zürich", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Eberhard-Karls-Universität Tübingen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Freie Universität Berlin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Center for Integrative Bioinformatics (CiBi)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "cibi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "General Mailinglist", "email": "open-ms-general@lists.sourceforge.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "General Mailinglist", "email": "open-ms-general@lists.sourceforge.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Hannes Röst", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-0990-7488", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "samwein", "additionDate": "2016-01-19T16:39:56Z", "lastUpdate": "2025-04-30T11:39:30.251890Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pyOpenMS", "description": "Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data.", "homepage": "https://github.com/OpenMS/pyopenms-extra/blob/master/docs/source/index.rst", "biotoolsID": "pyOpenMS", "biotoolsCURIE": "biotools:pyOpenMS", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OpenMS/pyopenms-extra", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/OpenMS/pyopenms-extra/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://pyopenms.readthedocs.io", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.7287/PEERJ.PREPRINTS.27736", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Hannes L. Rost", "email": "hannes.rost@utoronto.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "samwein", "additionDate": "2019-08-09T13:16:33Z", "lastUpdate": "2025-04-30T11:39:29.549782Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenSWATH", "description": "OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS.", "homepage": "http://www.openswath.org", "biotoolsID": "OpenSWATH", "biotoolsCURIE": "biotools:OpenSWATH", "version": [ "OpenMS 2.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental 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Rosenberger", "email": "gr2578@cumc.columbia.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "samwein", "additionDate": "2019-06-18T11:06:01Z", "lastUpdate": "2025-04-30T11:39:29.102190Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenPepXL", "description": "An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.\n\nProtein-Protein Cross-Linking (OpenPepXL) – OpenMS.\n\nOpenPepXL is a protein-protein cross-link identification tool implemented in C++ as part of OpenMS. It works with all uncleavable labeled and label-free cross-linkers but not (yet) with cleavable ones.", "homepage": "https://openms.org/openpepxl", "biotoolsID": "openpepxl", "biotoolsCURIE": "biotools:openpepxl", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.openms.de/openpepxl", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/MCP.TIR120.002186", "pmid": "33067342", "pmcid": "PMC7710140", "type": [], "version": null, "note": null, "metadata": { "title": "OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS", "abstract": "© 2020 Netz et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc.Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared with other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Because of efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of noncleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a data set from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenPepXL finds from 7% to over 50% more unique residue pairs (URPs) than other tools. On data sets with available high-resolution structures for cross-link validation OpenPepXL reports from 7% to over 40% more structurally validated URPs than other tools. Additionally, we used a synthetic peptide data set that allows objective validation of cross-links without relying on structural information and found that OpenPepXL reports at least 12% more validated URPs than other tools. It has been built as part of the OpenMS suite of tools and supports Windows, macOS, and Linux operating systems. OpenPepXL also supports the MzIdentML 1.2 format for XL-MS identification results. It is freely available under a three-clause BSD license at https://openms.org/openpepxl.", "date": "2020-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Netz E." }, { "name": "Dijkstra T.M.H." }, { "name": "Sachsenberg T." }, { "name": "Zimmermann L." }, { "name": "Walzer M." }, { "name": "Monecke T." }, { "name": "Ficner R." }, { "name": "Dybkov O." }, { "name": "Urlaub H." }, { "name": "Kohlbacher O." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Eugen Netz", "email": "eugen.netz@tuebingen.mpg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Oliver Kohlbacher", "email": "oliver.kohlbacher@uni-tuebingen.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "samwein", "additionDate": "2021-01-18T11:10:26Z", "lastUpdate": "2025-04-30T11:39:28.349250Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "compareMS2", "description": "compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.", "homepage": "https://github.com/524D/compareMS2", "biotoolsID": "comparems2", "biotoolsCURIE": "biotools:comparems2", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C", "JavaScript" ], "license": "MIT", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/524D/compareMS2", "type": [ "Repository" ], "note": null }, { "url": "https://www.ms-utils.org/compareMS2.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://research-software-directory.org/software/comparems2", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.html", "type": "Binaries", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://github.com/524D/compareMS2/tree/main/src", "type": "Source code", "note": null, "version": "2.0" }, { "url": "https://github.com/524D/compareMS2/tree/main", "type": "Binaries", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://www.ms-utils.org/compareMS2.html", "type": [ "General", "Command-line options" ], "note": null }, { "url": "https://github.com/524D/compareMS2", "type": [ "General", "User manual", "Command-line options", "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.6162", "pmid": "22368051", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Molecular phylogenetics by direct comparison of tandem mass spectra", "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.", "date": "2012-04-15T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Palmblad M." }, { "name": "Deelder A.M." } ], "journal": "Rapid Communications in Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.2c00457", "pmid": "36173614", "pmcid": "PMC9903320", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets", "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.", "date": "2023-02-03T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Marissen R." }, { "name": "Varunjikar M.S." }, { "name": "Laros J.F.J." }, { "name": "Rasinger J.D." }, { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.1c00528", "pmid": "34523928", "pmcid": "PMC8491155", "type": [ "Review" ], "version": "2.0", "note": null, "metadata": { "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics", "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.", "date": "2021-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": "https://www.lumc.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Support" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": "https://github.com/magnuspalmblad", "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Documentor" ], "note": null }, { "name": "Rob Marissen", "email": null, "url": "https://github.com/524D", "orcidid": "https://orcid.org/0000-0002-1220-9173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2025-04-16T14:22:04.957317Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "neXtProt", "description": "neXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.", "homepage": "https://www.expasy.org/archives/nextprot", "biotoolsID": "nextprot", "biotoolsCURIE": "biotools:nextprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "Rare Disease", "Proteomics" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/calipho-sib/", "type": [ "Repository" ], "note": "neXtProt software repository with issue tracking" }, { "url": "https://twitter.com/nextprot_news", "type": [ "Social media" ], "note": "neXtProt release news, publications, presentations, tips and more. DM us with feedback!" }, { "url": "https://www.expasy.org/resources/nextprot", "type": [ "Software catalogue" ], "note": "neXtProt entry in Expasy" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkz995", "pmid": "31724716", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The neXtProt knowledgebase in 2020: Data, tools and usability improvements", "abstract": "The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.", "date": "2020-01-01T00:00:00Z", "citationCount": 155, "authors": [ { "name": "Zahn-Zabal M." }, { "name": "Michel P.-A." }, { "name": "Gateau A." }, { "name": "Nikitin F." }, { "name": "Schaeffer M." }, { "name": "Audot E." }, { "name": "Gaudet P." }, { "name": "Duek P.D." }, { "name": "Teixeira D." }, { "name": "De Laval V.R." }, { "name": "Samarasinghe K." }, { "name": "Bairoch A." }, { "name": "Lane L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1179", "pmid": "22139911", "pmcid": "PMC3245017", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NeXtProt: A knowledge platform for human proteins", "abstract": "neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Lane L." }, { "name": "Argoud-Puy G." }, { "name": "Britan A." }, { "name": "Cusin I." }, { "name": "Duek P.D." }, { "name": "Evalet O." }, { "name": "Gateau A." }, { "name": "Gaudet P." }, { "name": "Gleizes A." }, { "name": "Masselot A." }, { "name": "Zwahlen C." }, { "name": "Bairoch A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Support", "email": "support@nextprot.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pascale Gaudet", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-1813-6857", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "SIB", "additionDate": "2015-01-21T13:30:06Z", "lastUpdate": "2025-04-02T08:05:19.163091Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "mzahn", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WeSA", "description": "WeSA, (weighted socioaffinity), is a statistical score which can rank results from protein experiments of the bait-prey type, e.g. affinity purification, immunoprecipitation or proximity labelling.\n\nYou can enter lists of interacting proteins according to the results of your experiment. Input your raw data before any filtering is done.\n\nAs a result you will get a re-ordered list of scores which allows one to understand which interactions are more likely than others based on what previous experiments can add to your data.", "homepage": "https://wesa.russelllab.org/", "biotoolsID": "we_sa", "biotoolsCURIE": "biotools:we_sa", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3957", "term": "Protein interaction experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/russelllab/wesa", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://wesa.russelllab.org/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae423", "pmid": "38795065", "pmcid": "PMC11223876", "type": [], "version": null, "note": null, "metadata": { "title": "WeSA: A web server for improving analysis of affinity proteomics data", "abstract": "Protein-protein interaction experiments still yield many false positive interactions. The socioaffinity metric can distinguish true protein-protein interactions from noise based on available data. Here, we present WeSA (Weighted SocioAffinity), which considers large datasets of interaction proteomics data (IntAct, BioGRID, the BioPlex) to score human protein interactions and, in a statistically robust way, flag those (even from a single experiment) that are likely to be false positives. ROC analysis (using CORUM-PDB positives and Negatome negatives) shows that WeSA improves over other measures of interaction confidence. WeSA shows consistently good results over all datasets (up to: AUC = 0.93 and at best threshold: TPR = 0.84, FPR = 0.11, Precision = 0.98). WeSA is freely available without login (wesa.russelllab.org). Users can submit their own data or look for organized information on human protein interactions using the web server. Users can either retrieve available information for a list of proteins of interest or calculate scores for new experiments. The server outputs either pre-computed or updated WeSA scores for the input enriched with information from databases. The summary is presented as a table and a network-based visualization allowing the user to remove those nodes/edges that the method considers spurious.", "date": "2024-07-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Shtetinska M.M." }, { "name": "Gonzalez-Sanchez J.-C." }, { "name": "Beyer T." }, { "name": "Boldt K." }, { "name": "Ueffing M." }, { "name": "Russell R.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [], "owner": "Pub2Tools", "additionDate": "2025-03-28T11:13:12.813456Z", "lastUpdate": "2025-03-28T12:14:32.901305Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "prolfquapp", "description": "A command-line tool for differential expression analysis in quantitative proteomics", "homepage": "https://github.com/prolfqua/prolfquapp", "biotoolsID": "prolfquapp", "biotoolsCURIE": "biotools:prolfquapp", "version": [ "0.1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": "./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN\n# and again you run the version within the docker container with\n# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN" }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/prolfqua/prolfquapp", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/prolfqua/prolfquapp/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6", "type": "Downloads page", "note": null, "version": "0.1.6" } ], "documentation": [ { "url": "https://github.com/prolfqua/prolfquapp/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.4c00911", "pmid": null, "pmcid": null, "type": [], "version": "0.0.6", "note": null, "metadata": { "title": "prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics", "abstract": "Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The prolfquapp addresses this challenge by providing a command-line interface that simplifies DEA, making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems. Prolfquapp streamlines data processing and result visualization by generating dynamic HTML reports that facilitate the exploration of differential expression results. These reports allow for investigating complex experiments, such as those involving repeated measurements or multiple explanatory variables. Additionally, prolfquapp supports various output formats, including XLSX files, SummarizedExperiment objects and rank files, for further interactive analysis using spreadsheet software, the exploreDE Shiny application, or gene set enrichment analysis software, respectively. By leveraging advanced statistical models from the prolfqua R package, prolfquapp offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs.", "date": "2025-02-07T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wolski W.E." }, { "name": "Grossmann J." }, { "name": "Schwarz L." }, { "name": "Leary P." }, { "name": "Turker C." }, { "name": "Nanni P." }, { "name": "Schlapbach R." }, { "name": "Panse C." } ], "journal": "Journal of Proteome Research" } } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2025-02-28T15:04:33.594183Z", "lastUpdate": "2025-03-28T10:18:25.715685Z", "editPermission": { "type": "group", "authors": [ "thatmariia" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetIDfyR", "description": "Open-Source R Package to Decipher Small-Molecule Drugs Metabolism Through High Resolution Mass Spectrometry.\n\nMetIDfyR is an open-source, cross-platform and versatile R script to predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest.", "homepage": "https://github.com/agnesbrnb/MetIDfyR", "biotoolsID": "metidfyr", "biotoolsCURIE": "biotools:metidfyr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] }, { "data": { "uri": "http://edamontology.org/data_0846", "term": "Chemical formula" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" }, { "uri": "http://edamontology.org/topic_3370", "term": "Analytical chemistry" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/agnesbrnb/MetIDfyR", "type": [ "Quick start guide", "Installation instructions", "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.0c02281", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MetIDfyR: An Open-Source R Package to Decipher Small-Molecule Drug Metabolism through High-Resolution Mass Spectrometry", "abstract": "With recent advances in analytical chemistry, liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential tool for metabolite discovery and detection. Even if most of the common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, complicating metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited. In this article, we present MetIDfyR, an open-source and cross-platform R package for in silico drug phase I/II biotransformation prediction and mass-spectrometric data mining. MetIDfyR has proven its efficacy for advanced metabolite identification in semi-complex and complex mixtures in in vitro or in vivo drug studies and is freely available at github.com/agnesblch/MetIDfyR.", "date": "2020-10-06T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Delcourt V." }, { "name": "Barnabe A." }, { "name": "Loup B." }, { "name": "Garcia P." }, { "name": "Andre F." }, { "name": "Chabot B." }, { "name": "Trevisiol S." }, { "name": "Moulard Y." }, { "name": "Popot M.-A." }, { "name": "Bailly-Chouriberry L." } ], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "agnesbarnabe", "additionDate": "2021-01-18T09:08:27Z", "lastUpdate": "2025-02-27T15:46:01.807140Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProteoMaker", "description": "ProteoMaker is a platform for the generation of an in-silico bottom-up proteomics data set with a ground truth on the level of proteoforms.", "homepage": "https://github.com/computproteomics/ProteoMaker", "biotoolsID": "proteomaker", "biotoolsCURIE": "biotools:proteomaker", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3566", "term": "Simulated gene expression data generation" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1238", "term": "Proteolytic digest" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] }, { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3524", "term": "Simulation experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://computproteomics.bmb.sdu.dk/app_direct/ProteoMaker", "type": [ "Service" ], "note": "Web application" } ], "download": [ { "url": "https://github.com/computproteomics/ProteoMaker", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "veitveit11", "additionDate": "2025-01-31T17:19:47.094256Z", "lastUpdate": "2025-01-31T17:19:47.096981Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaboMAPS", "description": "Pathway sharing and multi-omics data visualization in metabolic context.\n\nMetaboMAPS is a web project for manipulating metabolic pathways in SVG format. MetaboMAPS consists of two main parts: the visualization tool, where users can plot their own data set, and the plot box editor, where users can add or change the areas for visualization (plot boxes) and assign identifiers to them.", "homepage": "https://metabomaps.brenda-enzymes.org", "biotoolsID": "metabomaps", "biotoolsCURIE": "biotools:metabomaps", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_3929", "term": "Metabolic pathway prediction" }, { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "JavaScript" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/JuliaHelmecke/MetaboMAPS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/F1000RESEARCH.23427.1", "pmid": "32765840", "pmcid": "PMC7383707", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Meina Neumann-Schaal", "email": "meina.neumann-schaal@dsmz.de", "url": null, "orcidid": "https://orcid.org/0000-0002-1641-019X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Niclaskn", "additionDate": "2021-01-18T10:23:20Z", "lastUpdate": "2025-01-23T15:00:32.268669Z", "editPermission": { "type": "group", "authors": [ "JKoblitz" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PHIStruct", "description": "PHIStruct is a phage-host interaction prediction tool that uses structure-aware protein embeddings to represent the receptor-binding proteins (RBPs) of phages. \n\nBy incorporating structure information, it presents improvements over using sequence-only protein embeddings and feature-engineered sequence properties — especially for phages with RBPs that have low sequence similarity to those of known phages.", "homepage": "https://github.com/bioinfodlsu/PHIStruct", "biotoolsID": "phistruct", "biotoolsCURIE": "biotools:phistruct", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Predicts the host genus of a phage given its receptor-binding protein sequences", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Repository" ], "note": null }, { "url": "http://phistruct.bioinfodlsu.com/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Installation instructions", "Quick start guide", "Citation instructions", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf016", "pmid": "39804673", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Mark Edward M. 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It presents improvements over using handcrafted (manually feature-engineered) sequence properties and eliminates the need to manually extract and select features from phage sequences.", "homepage": "https://github.com/bioinfodlsu/phage-host-prediction", "biotoolsID": "phiembed", "biotoolsCURIE": "biotools:phiembed", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Predicts the host genus of a phage given its receptor-binding protein sequences", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": [ "Repository" ], "note": null }, { "url": "http://phiembed.bioinfodlsu.com/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/bioinfodlsu/phage-host-prediction", "type": [ "Installation instructions", "Quick start guide", "Citation instructions", "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0289030", "pmid": "37486915", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Protein embeddings improve phage-host interaction prediction", "abstract": "With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage’s receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.", "date": "2023-07-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Gonzales M.E.M." }, { "name": "Ureta J.C." }, { "name": "Shrestha A.M.S." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Mark Edward M. Gonzales", "email": "gonzales.markedward@gmail.com", "url": "https://github.com/memgonzales", "orcidid": "https://orcid.org/0000-0001-5050-3157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Research Assistant, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Jennifer C. Ureta", "email": "jennifer.ureta@gmail.com", "url": "https://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=en", "orcidid": "https://orcid.org/0000-0003-0427-5311", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Faculty, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" }, { "name": "Anish M.S. Shrestha", "email": "anish.shrestha@dlsu.edu.ph", "url": "https://a-transposable-element.com/", "orcidid": "https://orcid.org/0000-0002-9192-9709", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Head, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines" } ], "owner": "memgonzales", "additionDate": "2024-05-05T10:53:14.688391Z", "lastUpdate": "2025-01-14T09:13:55.932761Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "scp", "description": "Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.", "homepage": "https://uclouvain-cbio.github.io/scp/", "biotoolsID": "scp", "biotoolsCURIE": "biotools:scp", "version": [ "1.16.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "recetox-specdatri", "additionDate": "2025-01-09T15:45:12.825558Z", "lastUpdate": "2025-01-11T12:06:29.826828Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ESIprot", "description": "Charge state determination and molecular weight calculation for low resolution electrospray ionization data.", "homepage": "https://nube-gran.de/esiprot", "biotoolsID": "esiprot", "biotoolsCURIE": "biotools:esiprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0398", "term": "Protein molecular weight calculation" }, { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.bioprocess.org/esiprot/esiprot_form.php", "type": [ "Mirror" ], "note": null }, { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null }, { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.4384", "pmid": "20049890", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ESIprot: A universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data", "abstract": "Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2Da, the relative errors below 30ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software. © 2010 John Wiley & Sons, Ltd.", "date": "2010-01-01T00:00:00Z", "citationCount": 75, "authors": [ { "name": "Winkler R." } ], "journal": "Rapid Communications in Mass Spectrometry" } } ], "credit": [ { "name": "Robert Winkler", "email": "robert.winkler@ira.cinvestav.mx", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:50:59Z", "lastUpdate": "2024-12-13T13:53:01.317118Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PolySTest", "description": "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.", "homepage": "http://computproteomics.bmb.sdu.dk/Apps/PolySTest", "biotoolsID": "PolySTest", "biotoolsCURIE": "biotools:PolySTest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_3905", "term": "Histogram" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bitbucket.org/veitveit/polystest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/mcp.RA119.001777", "pmid": "32424025", "pmcid": "PMC8015005", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "veits@bmb.sdu.dk", "additionDate": "2019-11-14T19:27:27Z", "lastUpdate": "2024-11-25T16:09:23.465736Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "2D-PAGE", "description": "2D-PAGE database.", "homepage": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi", "biotoolsID": "2d-page", "biotoolsCURIE": "biotools:2d-page", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2373", "term": "Spot ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2091", "term": "Accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1519", "term": "Peptide molecular weights" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1528", "term": "Protein isoelectric point" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0897", "term": "Protein property" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0942", "term": "2D PAGE image" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1528", "term": "Protein isoelectric point" }, "format": [] } ], "note": "This is the main interface of the Make2D-DB II tool to query SIENA 2D-DATABASE. Search by accession number or entry name (AC or ID),\nby description, or UniProtKB/Swiss-Prot keywords. General information, 2D-gel spot location and picture of gel.", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "DRCAT", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "University of Siena, Italy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "DRCAT", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": "Luca Bini", "email": "bini@unisi.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "DRCAT", "additionDate": "2015-09-11T17:01:36Z", "lastUpdate": "2024-11-25T14:17:26.650772Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3dLOGO", "description": "3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.", "homepage": "http://3dlogo.uniroma2.it/3dLOGO/home.html", "biotoolsID": "3dlogo", "biotoolsCURIE": "biotools:3dlogo", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0448", "term": "Sequence alignment analysis (conservation)" }, { "uri": "http://edamontology.org/operation_0245", "term": "Protein structural motif recognition" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkm228", "pmid": "17488847", "pmcid": "PMC1933223", "type": [], "version": null, "note": null, "metadata": { "title": "3dLOGO: A web server for the identification, analysis and use of conserved protein substructures", "abstract": "3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/. © 2007 The Author(s).", "date": "2007-07-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Via A." }, { "name": "Peluso D." }, { "name": "Gherardini P.F." }, { "name": "De Rinaldis E." }, { "name": "Colombo T." }, { "name": "Ausiello G." }, { "name": "Helmer-Citterich M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1006/jmbi.1998.2248", "pmid": "9837739", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Three-dimensional profiles: A new tool to identify protein surface similarities", "abstract": "We report a procedure for the description and comparison of protein surfaces, which is based on a three-dimensional (3D) transposition of the profile method for sensitive protein homology sequence searches. Although the principle of the method can be applied to detect similarities to a single protein surface, the possibility of extending this approach to protein families displaying common structural and/or functional properties, makes it a more powerful tool. In analogy to profiles derived from the multiple alignment of protein sequences, we derive a 3D surface profile from a protein structure or from a multiple structure alignment of several proteins. The 3D profile is used to screen the protein structure database, searching for similar protein surfaces. The application of the procedure to SH2 and SH3 binding pockets and to the nucleotide binding pocket associated with the p-loop structural motif is described. The SH2 and SH3 3D profiles can identify all the SH2 and SH3 binding regions present in the test dataset; the p-loop 3D profile is able to recognize all the p-loop-containing proteins present in the test dataset. Analysis of the p-loop 3D profile allowed the identification of a positive charge whose position is conserved in space but not in sequence. The best ranking non-p-loop-containing protein is an ADP-forming succinyl coenzyme A synthetase, whose nucleotide-binding region has not yet been identified.", "date": "1998-12-11T00:00:00Z", "citationCount": 42, "authors": [ { "name": "De Rinaldis M." }, { "name": "Ausiello G." }, { "name": "Cesareni G." }, { "name": "Helmer-Citterich M." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1186/1471-2105-5-50", "pmid": "15119965", "pmcid": "PMC420233", "type": [], "version": null, "note": null, "metadata": { "title": "A structural study for the optimisation of functional motifs encoded in protein sequences", "abstract": "Background. A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that - at least in some cases - the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results. Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion. Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available. © 2004 Via and Helmer-Citterich, licensee BioMed Central Ltd.", "date": "2004-04-30T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Via A." }, { "name": "Helmer-Citterich M." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/1471-2105-6-s4-s5", "pmid": "16351754", "pmcid": "PMC1866380", "type": [], "version": null, "note": null, "metadata": { "title": "Query3d: A new method for high-throughput analysis of functional residues in protien structures", "abstract": "Background: The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Results: Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. Conclusion: With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.", "date": "2005-12-01T00:00:00Z", "citationCount": 50, "authors": [ { "name": "Ausiello G." }, { "name": "Via A." }, { "name": "Helmer-Citterich M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [], "owner": "ELIXIR-EE", "additionDate": "2017-02-14T09:34:42Z", "lastUpdate": "2024-11-25T14:17:22.357136Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3Omics", "description": "A web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.", "homepage": "https://3omics.cmdm.tw/", "biotoolsID": "3omics", "biotoolsCURIE": "biotools:3omics", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://3omics.cmdm.tw/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1752-0509-7-64", "pmid": "23875761", "pmcid": "PMC3723580", "type": [], "version": null, "note": null, "metadata": { "title": "3Omics: A web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data", "abstract": "Background: Integrative and comparative analyses of multiple transcriptomics, proteomics and metabolomics datasets require an intensive knowledge of tools and background concepts. Thus, it is challenging for users to perform such analyses, highlighting the need for a single tool for such purposes. The 3Omics one-click web tool was developed to visualize and rapidly integrate multiple human inter- or intra-transcriptomic, proteomic, and metabolomic data by combining five commonly used analyses: correlation networking, coexpression, phenotyping, pathway enrichment, and GO (Gene Ontology) enrichment.Results: 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for all transcripts, proteins and metabolites. If only two of three omics datasets are input, then 3Omics supplements the missing transcript, protein or metabolite information related to the input data by text-mining the PubMed database. 3Omics' coexpression analysis assists in revealing functions shared among different omics datasets. 3Omics' phenotype analysis integrates Online Mendelian Inheritance in Man with available transcript or protein data. Pathway enrichment analysis on metabolomics data by 3Omics reveals enriched pathways in the KEGG/HumanCyc database. 3Omics performs statistical Gene Ontology-based functional enrichment analyses to display significantly overrepresented GO terms in transcriptomic experiments. Although the principal application of 3Omics is the integration of multiple omics datasets, it is also capable of analyzing individual omics datasets. The information obtained from the analyses of 3Omics in Case Studies 1 and 2 are also in accordance with comprehensive findings in the literature.Conclusions: 3Omics incorporates the advantages and functionality of existing software into a single platform, thereby simplifying data analysis and enabling the user to perform a one-click integrated analysis. Visualization and analysis results are downloadable for further user customization and analysis. The 3Omics software can be freely accessed at http://3omics.cmdm.tw. © 2013 Kuo et al.; licensee BioMed Central Ltd.", "date": "2013-07-13T00:00:00Z", "citationCount": 148, "authors": [ { "name": "Kuo T.-C." }, { "name": "Tian T.-F." }, { "name": "Tseng Y.J." } ], "journal": "BMC Systems Biology" } } ], "credit": [ { "name": "Yufeng Jane Tseng", "email": "yjtseng@csie.ntu.edu.tw", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-17T19:04:18Z", "lastUpdate": "2024-11-25T14:17:20.979256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ADEPTS", "description": "Software package for peptide identification using two different types of MS/MS spectra.", "homepage": "https://cs.uwaterloo.ca/~l22he/", "biotoolsID": "adepts", "biotoolsCURIE": "biotools:adepts", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/adepts-advanced-peptide-de-novo-sequencing-with-a-pair-of-tandem-mass-spectra.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1142/s0219720010005099", "pmid": "21121022", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Adepts: Advanced peptide de novo sequencing with a pair of tandem mass spectra", "abstract": "De novo sequencing is an important task in proteomics to identify novel peptide sequences. Traditionally, only one MS/MS spectrum is used for the sequencing of a peptide; however, the use of multiple spectra of the same peptide with different types of fragmentation has the potential to significantly increase the accuracy and practicality of de novo sequencing. Research into the use of multiple spectra is in a nascent stage. We propose a general framework to combine the two different types of MS/MS data. Experiments demonstrate that our method significantly improves the de novo sequencing of existing software. © 2010 Imperial College Press.", "date": "2010-12-01T00:00:00Z", "citationCount": 29, "authors": [ { "name": "He L." }, { "name": "Ma B." } ], "journal": "Journal of Bioinformatics and Computational Biology" } } ], "credit": [ { "name": null, "email": null, "url": "https://cs.uwaterloo.ca/~l22he/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:34Z", "lastUpdate": "2024-11-25T14:17:19.618187Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ALL-P", "description": "Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.", "homepage": "http://pappso.inra.fr/bioinfo/all_p/index.php", "biotoolsID": "all-p", "biotoolsCURIE": "biotools:all-p", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3321", "term": "Molecular genetics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/all-p-including-shared-peptides-estimating-protein-abundances.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://pappso.inra.fr/bioinfo/all_p/download.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201100660", "pmid": "22833229", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Including shared peptides for estimating protein abundances: A significant improvement for quantitative proteomics", "abstract": "Inferring protein abundances from peptide intensities is the key step in quantitative proteomics. The inference is necessarily more accurate when many peptides are taken into account for a given protein. Yet, the information brought by the peptides shared by different proteins is commonly discarded. We propose a statistical framework based on a hierarchical modeling to include that information. Our methodology, based on a simultaneous analysis of all the quantified peptides, handles the biological and technical errors as well as the peptide effect. In addition, we propose a practical implementation suitable for analyzing large data sets. Compared to a method based on the analysis of one protein at a time (that does not include shared peptides), our methodology proved to be far more reliable for estimating protein abundances and testing abundance changes. The source codes are available at http://pappso.inra.fr/bioinfo/all_p/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.", "date": "2012-09-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Blein-Nicolas M." }, { "name": "Xu H." }, { "name": "de Vienne D." }, { "name": "Giraud C." }, { "name": "Huet S." }, { "name": "Zivy M." } ], "journal": "Proteomics" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.inra.fr/les_recherches/annuaires/autres/microbiologie/pappso_plate_forme_d_analyses_proteomiques_de_paris_sud_ouest", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:41Z", "lastUpdate": "2024-11-25T14:17:18.441827Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AMYLPRED", "description": "Consensus prediction method for identifying possible amyloidogenic regions in protein sequences.", "homepage": "http://aias.biol.uoa.gr/AMYLPRED/", "biotoolsID": "amylpred", "biotoolsCURIE": "biotools:amylpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/amylpred-a-consensus-method-for-amyloid-propensity-prediction.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://aias.biol.uoa.gr/AMYLPRED/login.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1472-6807-9-44", "pmid": "19589171", "pmcid": "PMC2714319", "type": [], "version": null, "note": null, "metadata": { "title": "Amyloidogenic determinants are usually not buried", "abstract": "Background. Amyloidoses are a group of usually fatal diseases, probably caused by protein misfolding and subsequent aggregation into amyloid fibrillar deposits. The mechanisms involved in amyloid fibril formation are largely unknown and are the subject of current, intensive research. In an attempt to identify possible amyloidogenic regions in proteins for further experimental investigation, we have developed and present here a publicly available online tool that utilizes five different and independently published methods, to form a consensus prediction of amyloidogenic regions in proteins, using only protein primary structure data. Results. It appears that the consensus prediction tool is slightly more objective than individual prediction methods alone and suggests several previously not identified amino acid stretches as potential amyloidogenic determinants, which (although several of them may be overpredictions) require further experimental studies. The tool is available at: http://biophysics.biol.uoa.gr/AMYLPRED. Utilizing molecular graphics programs, like O and PyMOL, as well as the algorithm DSSP, it was found that nearly all experimentally verified amyloidogenic determinants (short peptide stretches favouring aggregation and subsequent amyloid formation), and several predicted, with the aid of the tool AMYLPRED, but not experimentally verified amyloidogenic determinants, are located on the surface of the relevant amyloidogenic proteins. This finding may be important in efforts directed towards inhibiting amyloid fibril formation. Conclusion. The most significant result of this work is the observation that virtually all, to date, experimentally determined amyloidogenic determinants and the majority of predicted, but not yet experimentally verified short amyloidogenic stretches, lie 'exposed' on the surface of the relevant amyloidogenic proteins, and also several of them have the ability to act as conformational 'switches'. Experiments, focused on these fragments, should be performed to test this idea. © 2009 Frousios et al; licensee BioMed Central Ltd.", "date": "2009-07-30T00:00:00Z", "citationCount": 128, "authors": [ { "name": "Frousios K.K." }, { "name": "Iconomidou V.A." }, { "name": "Karletidi C.-M." }, { "name": "Hamodrakas S.J." } ], "journal": "BMC Structural Biology" } } ], "credit": [ { "name": null, "email": "shamodr@biol.uoa.gr", "url": "http://biophysics.biol.uoa.gr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:47Z", "lastUpdate": "2024-11-25T14:17:16.586759Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANARCI", "description": "Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.", "homepage": "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php", "biotoolsID": "anarci", "biotoolsCURIE": "biotools:anarci", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/anarci-antigen-receptor-numbering-and-receptor-classification.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv552", "pmid": "26424857", "pmcid": "PMC4708101", "type": [], "version": null, "note": null, "metadata": { "title": "ANARCI: Antigen receptor numbering and receptor classification", "abstract": "Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate residue positions, their definitions of position equivalence and their popularity within different scientific disciplines. However, currently no publicly available software exists that can apply all the most widely used schemes or for which an executable can be obtained under an open license. Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences. It can annotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMGT and AHo. Availability and implementation: ANARCI is available for download under GPLv3 license at opig.stats.ox.ac.uk/webapps/anarci. A web-interface to the program is available at the same address. Contact:", "date": "2016-01-15T00:00:00Z", "citationCount": 193, "authors": [ { "name": "Dunbar J." }, { "name": "Deane C.M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://opig.stats.ox.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:48Z", "lastUpdate": "2024-11-25T14:17:15.343704Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AnDom", "description": "Web tool that helps to assign structural domains to protein sequences and to classify them according to SCOP.", "homepage": "http://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.html", "biotoolsID": "andom", "biotoolsCURIE": "biotools:andom", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2996", "term": "Structure classification" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/andom-assign-structual-domains-protein-sequences.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://andom.bioapps.biozentrum.uni-wuerzburg.de/Usage_new.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ci010374r", "pmid": "11911710", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A versatile structural domain analysis server using profile weight matrices", "abstract": "The WEB tool \"AnDom\" assigns to a given protein sequence all experimentally determined structural domains contained within it, including multidomain and large proteins. The server uses profile specific matrices from custom generated multiple sequence alignments of all known SCOP domains (SCOP version 1.50). Prediction time is short allowing numerous applications for structural genomics including investigation of complex eucaryotic protein families. The WWW server is at http://www.bork.embl-heidelberg.de/AnDom, and profiles can be downloaded at ftp.bork.embl-heidelberg.de/pub/users/schmidt/AnDom.", "date": "2002-03-01T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Schmidt S." }, { "name": "Bork P." }, { "name": "Dandekar T." } ], "journal": "Journal of Chemical Information and Computer Sciences" } } ], "credit": [ { "name": "Dominik Schaack & Steffen Schmidt", "email": null, "url": "http://www.bork.embl.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:20Z", "lastUpdate": "2024-11-25T14:17:13.978877Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANM", "description": "Simple NMA tool for analysis of vibrational motions in molecular systems. It uses Elastic Network (EN) methodology and represents the system in the residue level.", "homepage": "http://anm.csb.pitt.edu/", "biotoolsID": "anm", "biotoolsCURIE": "biotools:anm", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics simulation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB", "Perl", "C" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/anm-2-0-aanm-1-1-adaptive-anisotropic-network-model-web-server.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://anm.csb.pitt.edu/anmdocs/Documentation2.1.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btu847", "pmid": "25568280", "pmcid": "PMC4410662", "type": [], "version": null, "note": null, "metadata": { "title": "The anisotropic network model web server at 2015 (ANM 2.0)", "abstract": "The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein-DNA/RNA and-ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces.", "date": "2015-05-01T00:00:00Z", "citationCount": 136, "authors": [ { "name": "Eyal E." }, { "name": "Lum G." }, { "name": "Bahar I." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.csb.pitt.edu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:49Z", "lastUpdate": "2024-11-25T14:17:12.623733Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AodPred", "description": "This tool was developed to identify antioxidant proteins based on the sequence information.", "homepage": "http://lin.uestc.edu.cn/server/AntioxiPred", "biotoolsID": "aodpred", "biotoolsCURIE": "biotools:aodpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/aodpred-identifying-antioxidant-proteins-by-using-optimal-dipeptide-compositions.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://lin.uestc.edu.cn/server/Aod/readme", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s12539-015-0124-9", "pmid": "26345449", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions", "abstract": "Antioxidant proteins are a kind of molecules that can terminate cellular and DNA damages caused by free radical intermediates. The use of antioxidant proteins for prevention of diseases has been intensively studied in recent years. Thus, accurate identification of antioxidant proteins is essential for understanding their roles in pharmacology. In this study, a support vector machine-based predictor called AodPred was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using feature selection method. It was observed by jackknife cross-validation test that AodPred can achieve an overall accuracy of 74.79 % in identifying antioxidant proteins. As a user-friendly tool, AodPred is freely accessible at http://lin.uestc.edu.cn/server/AntioxiPred. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results.", "date": "2016-06-01T00:00:00Z", "citationCount": 45, "authors": [ { "name": "Feng P." }, { "name": "Chen W." }, { "name": "Lin H." } ], "journal": "Interdisciplinary Sciences – Computational Life Sciences" } } ], "credit": [ { "name": "Hao Lin", "email": null, "url": "http://lin.uestc.edu.cn/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:25Z", "lastUpdate": "2024-11-25T14:17:11.389141Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "apComplex", "description": "Functions to estimate a bipartite graph of protein complex membership using AP-MS data.", "homepage": "http://bioconductor.org/packages/release/bioc/html/apComplex.html", "biotoolsID": "apcomplex", "biotoolsCURIE": "biotools:apcomplex", "version": [ "2.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0320", "term": "Protein structure assignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Proteomics", "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/apComplex_2.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/apComplex.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bti567", "pmid": "15998662", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Local modeling of global interactome networks", "abstract": "Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity-purification/mass-spectrometry (AP-MS) technologies measure different protein-protein relationships, and issues of completeness, sensitivity and specificity fuel debate over which is best for high-throughput 'interactome' data collection. Static graphs currently used to model Y2H and AP-MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function. Results: We apply the local modeling methodology proposed by Scholtens and Gentleman (2004) to two publicly available datasets and demonstrate its uses, interpretation and limitations. Specifically, we use this technology to address four major issues pertaining to protein-protein networks. (1) We motivate the need to move from static global interactome graphs to local protein complex models. (2) We formally show that accurate local interactome models require both Y2H and AP-MS data, even in idealized situations. (3) We briefly discuss experimental design issues and how bait selection affects interpretability of results. (4) We point to the implications of local modeling for systems biology including functional annotation, new complex prediction, pathway interactivity and coordination with gene-expression data. © The Author 2005. Published by Oxford University Press. All rights reserved.", "date": "2005-09-01T00:00:00Z", "citationCount": 66, "authors": [ { "name": "Scholtens D." }, { "name": "Vidal M." }, { "name": "Gentleman R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Denise Scholtens", "email": "dscholtens@northwestern.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:02Z", "lastUpdate": "2024-11-25T14:17:10.116176Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "APECS", "description": "Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.", "homepage": "https://trac.nbic.nl/apecs/", "biotoolsID": "apecs", "biotoolsCURIE": "biotools:apecs", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3524", "term": "Simulation experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/apecs-intensity-based-peptide-selection.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://trac.nbic.nl/apecs/wiki#no1", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/pr1006944", "pmid": "20836568", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples", "abstract": "LC-MALDI provides an often overlooked opportunity to exploit the separation between LC-MS and MS/MS stages of a 2D-LC-MS-based proteomics experiment, that is, by making a smarter selection for precursor fragmentation. Apex Peptide Elution Chain Selection (APECS) is a simple and powerful method for intensity-based peptide selection in a complex sample separated by 2D-LC, using a MALDI-TOF/TOF instrument. It removes the peptide redundancy present in the adjacent first-dimension (typically strong cation exchange, SCX) fractions by constructing peptide elution profiles that link the precursor ions of the same peptide across SCX fractions. Subsequently, the precursor ion most likely to fragment successfully in a given profile is selected for fragmentation analysis, selecting on precursor intensity and absence of adjacent ions that may cofragment. To make the method independent of experiment-specific tolerance criteria, we introduce the concept of the branching factor, which measures the likelihood of false clustering of precursor ions based on past experiments. By validation with a complex proteome sample of Arabidopsis thaliana, APECS identified an equivalent number of peptides as a conventional data-dependent acquisition method but with a 35% smaller work load. Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides. © 2010 American Chemical Society.", "date": "2010-11-05T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Gandhi T." }, { "name": "Fusetti F." }, { "name": "Wiederhold E." }, { "name": "Breitling R." }, { "name": "Poolman B." }, { "name": "Permentier H.P." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.nbic.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:51Z", "lastUpdate": "2024-11-25T14:17:08.762850Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }