ESIprotCharge state determination and molecular weight calculation for low resolution electrospray ionization data.https://nube-gran.de/esiprotesiprotbiotools:esiprotWeb applicationDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacPythonGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data format

http://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data format

http://www.bioprocess.org/esiprot/esiprot_form.phpMirrorhttp://ms-utils.orgSoftware cataloguehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprotGeneral10.1002/rcm.438420049890Robert Winklerrobert.winkler@ira.cinvestav.mxPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorBridgeDbBridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.http://bridgedb.github.io/bridgedbbiotools:bridgedb3.0.18Libraryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_2840ToxicologyMacLinuxWindowsJavaApache-2.0ProteomicsELIXIR-NLBIGCAT-UMBridgeDbRare DiseaseMatureFree of chargeInteroperabilityNetherlandshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1025Gene identifier

http://edamontology.org/data_1025Gene identifier

API for converting gene identifiers (Ensembl, Entrez) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifier

http://edamontology.org/data_0989Protein identifier

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1086Compound identifier

http://edamontology.org/data_1086Compound identifier

API for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem, etc) to identifiers from another database. Depends on an identifier-identifier mapping database or service supported by the API.https://github.com/bridgedb/BridgeDbRepositoryhttps://github.com/bridgedb/BridgeDb/issuesIssue trackerhttps://fosstodon.org/@bridgedbSocial mediahttps://bridgedb.github.io/pages/docs.htmlGeneralidentifiers.orgusesbioregistryuses10.1186/1471-2105-11-520047655PMC282467810.1007/978-3-319-11964-9_7Primary10.3897/rio.8.e83031PrimaryMaastricht UniversityInstituteProviderFusionWeb application for the integrative analysis of omics data providing a collection of new and established tools and visualization methods to support researchers in exploring multi-level omics data. The software focuses on data-rich high-throughout experiments from transcriptomics, proteomics and/or metabolomics, and offers convenient functionality for a) omics data manipulation, b) data analysis, c) cluster analysis, d) data visualization.https://fusion.cebitec.uni-bielefeld.defusionbiotools:fusionWeb applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacGPL-3.0de.NBITranscriptomicsde.NBI-BiGiProteomicsEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_2943Box-Whisker plot plottinghttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3744Multiple sample visualisationhttp://edamontology.org/operation_3463Gene expression correlationhttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2939Principal component plottinghttp://edamontology.org/operation_0533Gene to pathway mappinghttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3620xlsxhttps://fusion.cebitec.uni-bielefeld.de/QuickStartGuide.pdfUser manual10.2390/biecoll-jib-2016-29628187412Primaryfusion-service@cebitec.uni-bielefeld.dehttp://www.cebitec.uni-bielefeld.de/brf/index.php/fusionPersonPrimary contactSWISS-2DPAGEData on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.http://www.expasy.org/ch2d/swiss-2dpagebiotools:swiss-2dpageRRID:SCR_006946rridDatabase portalhttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifier

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_3021UniProt accession

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_3021UniProt accession

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2374Spot serial number

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2791Reference map name (SWISS-2DPAGE)

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2791Reference map name (SWISS-2DPAGE)

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2374Spot serial number

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

http://world-2dpage.expasy.org/swiss-2dpage/docs/manch2d.htmlGeneral10.1002/pmic.20030083015274128PrimarySIB Swiss Institute of BioinformaticsInstituteContributorhttp://world-2dpage.expasy.org/contactPersonPrimary contactomicRexposomeIt systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).http://bioconductor.org/packages/release/bioc/html/omicRexposome.htmlomicrexposomebiotools:omicrexposome1.2.0Libraryhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3308TranscriptomicsMacLinuxWindowsRMITBioConductorProteomicsFree of chargehttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_3809Differentially-methylated region identificationhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_0337Visualisationhttp://bioconductor.org/packages/omicRexposome/Mirrorhttp://bioconductor.org/packages/release/bioc/src/contrib/omicRexposome_1.2.0.tar.gzSoftware packagehttp://bioconductor.org/packages/release/bioc/manuals/omicRexposome/man/omicRexposome.pdfUser manualrexposomeuses10.1093/bioinformatics/btz52631243429Primary10.1038/s41467-022-34422-236411288PMC9678903UsageCarles Hernandez-Ferrercarles.hernandez@isglobal.orghttp://www.carleshf.comhttps://orcid.org/0000-0002-8029-7160PersonDeveloperXavier Escribà Montagutxavier.escriba@isglobal.orgPersonMaintainerJuan R Gonzalezjuanr.gonzalez@isglobal.orghttps://brge.isglobal.org/MetFusionApproach to combine the knowledge from spectral databases like MassBank with the multitude of candidates generated by fragmenters such as MetFrag. The functionality of the original MetFusion application has been integrated into MetFrag, MetFusion itself has been deactivated.http://msbi.ipb-halle.de/MetFusion/metfusionbiotools:metfusionWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172MetabolomicsWindowsMacLinuxLegacyhttp://edamontology.org/operation_3214Spectral analysishttps://msbi.ipb-halle.de/MetFusion/General10.1002/jms.312323494783mgerlich@ipb-halle.dePersonPrimary contactComplexBrowserComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.https://computproteomics.bmb.sdu.dk/app_direct/ComplexBrowser/ComplexBrowserbiotools:ComplexBrowser1.0Web applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityWindowsMacLinuxRProteomicsOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/operation_2940Scatter plot plottinghttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/operation_2938Dendrogram visualisationhttp://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_3463Expression correlation analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0906Protein interaction datahttp://edamontology.org/format_3752CSV

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3508PDF

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3508PDF

http://computproteomics.bmb.sdu.dk/Software cataloguehttps://bitbucket.org/michalakw/complexbrowser/src/master/Repositoryhttps://bitbucket.org/michalakw/complexbrowser/Source code1.0https://bitbucket.org/michalakw/complexbrowser/raw/dc9d8f0c8dff610e2f58e3cb5f5087d050df26f2/Manual.pdfUser manual10.1101/573774PrimaryVeit Schwämmleveits@bmb.sdu.dkPersonCliqueMSComputational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.https://github.com/osenan/cliqueMSCliqueMSbiotools:CliqueMS0.3.2Libraryhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacRC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3798Read binninghttp://edamontology.org/operation_3803Natural product identificationhttps://github.com/osenan/cliqueMS/issuesIssue trackerhttps://cran.r-project.org/src/contrib/Archive/cliqueMS/Source codehttps://github.com/osenan/cliqueMS/blob/master/vignettes/annotate_features.RmdTraining materialTutorial material10.1093/bioinformatics/btz20730903689PMC6792096PrimaryOriol Senanoriol.senan@urv.catPersonPrimary contactPeptideShakerPeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics datahttp://compomics.github.io/projects/peptide-shaker.htmlpeptideshakerbiotools:peptideshaker3.0.11Desktop applicationCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0644ProteomeMacLinuxJavaApache-2.0de.NBIProteomicsBioInfra.ProtOpen accesshttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_2992Protein structure imagehttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_3754GO-term enrichment datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2969Sequence imagehttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSV

https://github.com/compomics/peptide-shakerSource codehttp://compomics.github.io/projects/peptide-shaker.html#read-meGeneral10.1038/nbt.310925574629PrimaryBioInfra.ProtInstituteProviderDominik Kopczynskdominik.kopczynski@isas.dehttp://compomics.github.io/projects/peptide-shaker.htmlPersonPrimary contactOpenChromOpen source tool for mass spectrometry and chromatography.https://www.openchrom.net/openchrombiotools:openchromDesktop applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3370Analytical chemistryLinuxWindowsMacJavaEPL-1.0ms-utilsMaturehttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/data_0943Mass spectrometry spectrahttp://edamontology.org/format_1637dathttp://edamontology.org/format_3712Thermo RAWhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3650NetCDF

http://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_3244mzML

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3508PDF

http://ms-utils.orgSoftware cataloguehttps://openchrom.net/downloadDownloads pagehttps://github.com/OpenChrom/openchromSource codehttps://lablicate.com/marketplace/extensions/handbookUser manualhttps://github.com/OpenChrom/openchrom/wiki/faqFAQ10.1186/1471-2105-11-40520673335Philip Wenigphilip.wenig@gmx.netPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorMatthias Mailänderhttps://orcid.org/0000-0001-6114-0304PersonContributorProteinProspectorA suite of protein identification tools.http://prospector.ucsf.eduproteinprospectorbiotools:proteinprospectorRRID:SCR_014558rridWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3489Database managementLinuxWindowsMacms-utilsProteomicshttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3647Blind peptide database searchhttp://ms-utils.orgSoftware cataloguehttp://prospector.ucsf.edu/prospector/html/instruct/allman.htmUser manual10.1074/mcp.d500002-mcp20015937296PrimaryAdminppadmin@cgl.ucsf.eduPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorMake2D-DB IIMake2D-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.https://world-2dpage.expasy.org/make2ddb/make2d-db_iibiotools:make2d-db_iiWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxMacPerlProteomicshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3630Protein quantificationhttps://world-2dpage.expasy.org/make2ddb/1.Readme_main.htmlGeneral10.1002/pmic.20030048312923769PrimaryExPASy helpdeskhttps://www.expasy.org/supportPersonPrimary contactSwiss Mass AbacusCalculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.https://glycoproteome.expasy.org/swiss-mass-abacus/swiss_mass_abacusbiotools:swiss_mass_abacusWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0122Structural genomicshttp://edamontology.org/topic_0601Protein modificationsLinuxWindowsMacProteomicshttp://edamontology.org/operation_0417Protein post-translation modification site predictionhttps://glycoproteome.expasy.org/swiss-mass-abacus/GeneralExPASy helpdeskhttps://www.expasy.org/supportPersonPrimary contactGlydinGlydin' 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.https://glycoproteome.expasy.org/epitopes/glydinbiotools:glydinWeb applicationhttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_0417Protein post-translation modification site predictionhttps://glycoproteome.expasy.org/epitopes/GeneralExPASy helpdeskhttps://www.expasy.org/supportPersonPrimary contactPyteomicsFramework for proteomics data analysis, supporting mzML, MGF, pepXML and more.https://pyteomics.readthedocs.io/pyteomicsbiotools:pyteomics4.7.5Libraryhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacPythonApache-2.0Proteomicshttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3654mzXMLhttps://github.com/levitsky/pyteomicsRepositoryhttps://pypi.org/project/pyteomics/Software packagehttps://pyteomics.readthedocs.io/User manual10.1007/s13361-012-0516-623292976Primary10.1021/acs.jproteome.8b00717PrimaryPyteomics Google Groupspyteomics@googlegroups.comPersonMaintainerIssue trackerhttps://github.com/levitsky/pyteomics/issuesPersonPrimary contactPeptideProphetValidation of peptide identifications by MS/MS and database searches.http://peptideprophet.sourceforge.net/index.htmlpeptideprophetbiotools:peptideprophetCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityLinuxMacWindowsC++Perlms-utilsProteomicshttp://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3675Variant filteringhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_2331HTML

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_2331HTML

http://ms-utils.orgSoftware cataloguehttp://tools.proteomecenter.org/PeptideProphet.phpOtherhttps://sourceforge.net/projects/peptideprophet/Source codehttp://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideProphetGeneral10.1021/ac025747h12403597nesvi@umich.edunesvi@umich.eduPersonMaintainerakeller@systemsbiology.orgakeller@systemsbiology.orgPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorProteinProphetValidation of protein identifications by MS/MS and database searches.http://tools.proteomecenter.org/ProteinProphet.phpproteinprophetbiotools:proteinprophetCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityLinuxMacWindowsPerlCms-utilsProteomicshttp://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_3648Validation of peptide-spectrum matcheshttp://edamontology.org/operation_3644de Novo sequencinghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_2331HTML

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3468xls

http://ms-utils.orgSoftware cataloguehttps://sourceforge.net/projects/proteinprophet/Source codehttp://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphetGeneral14632076nesvi@umich.edunesvi@umich.eduPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorPIA - Protein Inference AlgorithmsThe 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.https://github.com/medbioinf/piapiabiotools:pia1.5Command-line toolLibraryDesktop applicationWorkflowhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3120Protein variantsLinuxWindowsMacJavaBSD-3-ClauseKNIMEde.NBIProteomicsBioInfra.ProtCUBiMed.RUBMatureFree of chargeOpen accessProteomicsGermanyhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0943Mass spectrometry spectrahttp://edamontology.org/format_3713Mascot .dat filehttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3684PRIDE XMLhttp://edamontology.org/format_3711X!Tandem XMLhttp://edamontology.org/format_3702MSFhttp://edamontology.org/format_3681mzTab

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_2206Sequence feature table format (text)http://edamontology.org/format_3765KNIME datatable formathttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3681mzTabhttp://edamontology.org/format_3247mzIdentML

http://edamontology.org/data_0989Protein identifierhttp://edamontology.org/format_2206Sequence feature table format (text)http://edamontology.org/format_3765KNIME datatable formathttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3681mzTabhttp://edamontology.org/format_3247mzIdentML

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 Proteinshttps://github.com/medbioinf/piaRepositoryhttps://github.com/mpc-bioinformatics/piaSource codehttp://bioconda.github.io/recipes/pia/README.htmlSoftware packagehttps://github.com/mpc-bioinformatics/pia/releasesBinarieshttps://hub.docker.com/r/julianusz/piaContainer filehttps://github.com/medbioinf/pia/wikiGeneralknimeuses10.1021/acs.jproteome.5b0012125938255Primary10.1021/acs.jproteome.8b0072330474983Julian Uszkoreitjulian.uszkoreit@rub.dehttp://orcid.org/0000-0001-7522-4007PersonPrimary contactDeveloperMaintainerCUBiMed.RUBcubimed@rub.deInstituteProviderOpenMSOpen 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.http://www.openms.deopenmsbiotools:openms2.0.0LibraryWorkbenchhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172MetabolomicsLinuxWindowsMacC++BSD-3-ClauseKNIMEde.NBIProteomicsOpenMSMatureFree of chargehttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_1812Parsinghttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3628Chromatographic alignmenthttp://edamontology.org/operation_3627Mass spectra calibrationhttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3633Retention time predictionhttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_3705Isotope-coded protein labelhttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/operation_3639iTRAQhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3635Labeled quantificationhttp://edamontology.org/operation_3359Splittinghttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/operation_3023Prediction and recognition (protein)http://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcMLhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcMLhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_2549OBOhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

http://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3652dtahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3764idXMLhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3246TraMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3683qcML

https://github.com/OpenMS/OpenMSRepositoryhttps://github.com/OpenMS/OpenMSSource codehttp://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/Binarieshttps://github.com/OpenMS/OpenMSSource codehttp://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.htmlGeneral10.1038/nmeth.395927575624Primary10.1007/978-1-60761-987-1_23OtherETH ZürichInstituteProviderEberhard-Karls-Universität TübingenInstituteProviderFreie Universität BerlinInstituteProviderCenter for Integrative Bioinformatics (CiBi)ConsortiumcibiInstituteProviderGeneral Mailinglistopen-ms-general@lists.sourceforge.netSupportGeneral Mailinglistopen-ms-general@lists.sourceforge.netPersonPrimary contactHannes Rösthttp://orcid.org/0000-0003-0990-7488PersonContributorOpenSWATHOpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS.http://www.openswath.orgOpenSWATHbiotools:OpenSWATHOpenMS 2.4.0Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacC++BSD-3-Clausems-utilsProteomicsFree of chargeOpen accesshttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_3710WIFF formathttp://edamontology.org/format_3245Mass spectrometry data format

http://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3621SQLite formathttp://edamontology.org/format_3654mzXML

http://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3628Chromatographic alignmenthttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3621SQLite formathttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/data_0943Mass spectrometry spectrahttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3246TraML

http://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3833featureXMLhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3621SQLite format

https://github.com/OpenSWATH/dockerRepositoryhttps://github.com/OpenMS/OpenMSRepositoryhttps://sourceforge.net/projects/open-ms/lists/open-ms-generalMailing listhttp://www.openswath.org/en/latest/docs/binaries.htmlSoftware packagehttp://www.openswath.org/en/latest/docs/sources.htmlSource codehttps://buildmedia.readthedocs.org/media/pdf/openswath/latest/openswath.pdfUser manual24727770Hannes Rösthroest@stanford.eduPersonGeorge Rosenbergergr2578@cumc.columbia.eduPersoncompareMS2compareMS2 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.https://github.com/524D/compareMS2comparems2biotools:comparems21.02.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacCJavaScriptMITms-utilsProteomicsMatureFree of chargeProteomicsNetherlandshttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_3272Species treehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_2855Distance matrixhttp://edamontology.org/format_1991megahttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1910newick

https://github.com/524D/compareMS2Repositoryhttps://www.ms-utils.org/compareMS2.htmlSoftware cataloguehttps://research-software-directory.org/software/comparems2Software cataloguehttp://www.ms-utils.org/compareMS2.cSource code1.0http://www.ms-utils.org/compareMS2.htmlBinaries1.0http://www.ms-utils.org/compareMS2.cSource code1.0https://github.com/524D/compareMS2/tree/main/srcSource code2.0https://github.com/524D/compareMS2/tree/mainBinaries2.0http://www.ms-utils.org/compareMS2.htmlGeneralCommand-line optionshttps://github.com/524D/compareMS2GeneralUser manualCommand-line optionsInstallation instructions10.1002/rcm.616222368051Primary1.010.1021/acs.jproteome.2c0045736173614PMC9903320Primary2.010.1021/acs.jproteome.1c0052834523928PMC8491155Review2.0lumc.nlhttps://www.lumc.nlInstituteSupportMagnus Palmbladmagnus.palmblad@gmail.comhttps://github.com/magnuspalmbladhttp://orcid.org/0000-0002-5865-8994PersonDeveloperPrimary contactDocumentorRob Marissenhttps://github.com/524Dhttps://orcid.org/0000-0002-1220-9173PersonDeveloperneXtProtneXtProt 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.https://www.expasy.org/archives/nextprotnextprotbiotools:nextprotDatabase portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_3120Protein variantshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacCC-BY-4.0Rare DiseaseProteomicsLegacyFree of chargeDataSwitzerlandhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2406Protein structure analysishttps://github.com/calipho-sib/RepositoryneXtProt software repository with issue trackinghttps://twitter.com/nextprot_newsSocial medianeXtProt release news, publications, presentations, tips and more. DM us with feedback!https://www.expasy.org/resources/nextprotSoftware catalogueneXtProt entry in Expasy10.1093/nar/gkz99531724716Primary10.1093/nar/gkr117922139911PMC3245017PrimarySIB Swiss Institute of BioinformaticsInstituteProviderSupportsupport@nextprot.orgPersonPrimary contactPascale Gaudethttp://orcid.org/0000-0003-1813-6857PersonContributor2D-PAGE2D-PAGE database.http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi2d-pagebiotools:2d-pageDatabase portalhttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacDRCATProteomicshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_2373Spot IDhttp://edamontology.org/data_2091Accessionhttp://edamontology.org/data_1519Peptide molecular weightshttp://edamontology.org/data_1528Protein isoelectric point

http://edamontology.org/data_0897Protein propertyhttp://edamontology.org/format_2331HTML

http://edamontology.org/data_09422D PAGE image

http://edamontology.org/data_1528Protein isoelectric point

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), by description, or UniProtKB/Swiss-Prot keywords. General information, 2D-gel spot location and picture of gel.http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgiGeneral10.1002/pmic.20030048312923769PrimaryUniversity of Siena, ItalyInstituteProviderDRCATProjectDocumentorLuca Binibini@unisi.itPersonPrimary contact3dLOGO3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.http://3dlogo.uniroma2.it/3dLOGO/home.html3dlogobiotools:3dlogoWeb applicationhttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0121ProteomicsProteomicshttp://edamontology.org/operation_0448Sequence alignment analysis (conservation)http://edamontology.org/operation_0245Protein structural motif recognitionhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2406Protein structure analysis10.1093/nar/gkm22817488847PMC193322310.1006/jmbi.1998.2248983773910.1186/1471-2105-5-5015119965PMC42023310.1186/1471-2105-6-s4-s516351754PMC18663803OmicsA web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.https://3omics.cmdm.tw/3omicsbiotools:3omicsWeb applicationhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_2815Human biologyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacPHPPerlProteomicshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3208Genome visualisationhttps://3omics.cmdm.tw/help.phpGeneral10.1186/1752-0509-7-6423875761PMC3723580Yufeng Jane Tsengyjtseng@csie.ntu.edu.twPersonPrimary contactADEPTSSoftware package for peptide identification using two different types of MS/MS spectra.https://cs.uwaterloo.ca/~l22he/adeptsbiotools:adeptsCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacProteomicshttp://edamontology.org/operation_3631Peptide identificationhttp://www.mybiosoftware.com/adepts-advanced-peptide-de-novo-sequencing-with-a-pair-of-tandem-mass-spectra.htmlSoftware catalogue10.1142/s021972001000509921121022https://cs.uwaterloo.ca/~l22he/PersonPrimary contactALL-PStatistical 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.http://pappso.inra.fr/bioinfo/all_p/index.phpall-pbiotools:all-pCommand-line toolhttp://edamontology.org/topic_3321Molecular geneticshttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_2406Protein structure analysishttp://www.mybiosoftware.com/all-p-including-shared-peptides-estimating-protein-abundances.htmlSoftware cataloguehttp://pappso.inra.fr/bioinfo/all_p/download.phpGeneral10.1002/pmic.20110066022833229http://www.inra.fr/les_recherches/annuaires/autres/microbiologie/pappso_plate_forme_d_analyses_proteomiques_de_paris_sud_ouestPersonPrimary contactAMYLPREDConsensus prediction method for identifying possible amyloidogenic regions in protein sequences.http://aias.biol.uoa.gr/AMYLPRED/amylpredbiotools:amylpredWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0081Structure analysisLinuxWindowsMacPythonProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0417Protein post-translation modification site predictionhttp://www.mybiosoftware.com/amylpred-a-consensus-method-for-amyloid-propensity-prediction.htmlSoftware cataloguehttp://aias.biol.uoa.gr/AMYLPRED/login.phpGeneral10.1186/1472-6807-9-4419589171PMC2714319shamodr@biol.uoa.grhttp://biophysics.biol.uoa.gr/PersonPrimary contactANARCITool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.phpanarcibiotools:anarciWeb applicationDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacPythonProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_2575Protein binding site predictionhttp://www.mybiosoftware.com/anarci-antigen-receptor-numbering-and-receptor-classification.htmlSoftware cataloguehttp://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.phpGeneral10.1093/bioinformatics/btv55226424857PMC4708101http://opig.stats.ox.ac.uk/PersonPrimary contactAnDomWeb tool that helps to assign structural domains to protein sequences and to classify them according to SCOP.http://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.htmlandombiotools:andomWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacProteomicshttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_2996Structure classificationhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/andom-assign-structual-domains-protein-sequences.htmlSoftware cataloguehttp://andom.bioapps.biozentrum.uni-wuerzburg.de/Usage_new.htmlGeneral10.1021/ci010374r11911710Dominik Schaack & Steffen Schmidthttp://www.bork.embl.de/PersonPrimary contactANMSimple NMA tool for analysis of vibrational motions in molecular systems. It uses Elastic Network (EN) methodology and represents the system in the residue level.http://anm.csb.pitt.edu/anmbiotools:anmWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2275Molecular modellingLinuxWindowsMacMATLABPerlCProteomicshttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2476Molecular dynamics simulationhttp://edamontology.org/operation_2406Protein structure analysishttp://www.mybiosoftware.com/anm-2-0-aanm-1-1-adaptive-anisotropic-network-model-web-server.htmlSoftware cataloguehttp://anm.csb.pitt.edu/anmdocs/Documentation2.1.htmlGeneral10.1093/bioinformatics/btu84725568280PMC4410662http://www.csb.pitt.edu/PersonPrimary contactAodPredThis tool was developed to identify antioxidant proteins based on the sequence information.http://lin.uestc.edu.cn/server/AntioxiPredaodpredbiotools:aodpredWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0474Protein structure predictionhttp://www.mybiosoftware.com/aodpred-identifying-antioxidant-proteins-by-using-optimal-dipeptide-compositions.htmlSoftware cataloguehttp://lin.uestc.edu.cn/server/Aod/readmeGeneral10.1007/s12539-015-0124-926345449Hao Linhttp://lin.uestc.edu.cn/PersonPrimary contactapComplexFunctions to estimate a bipartite graph of protein complex membership using AP-MS data.http://bioconductor.org/packages/release/bioc/html/apComplex.htmlapcomplexbiotools:apcomplex2.40.0Command-line toolLibraryhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacRGPL-3.0ProteomicsBioConductorFree of chargehttp://edamontology.org/operation_0320Protein structure assignmenthttp://bioconductor/packages/release/bioc/src/contrib/apComplex_2.40.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/apComplex.htmlUser manual10.1093/bioinformatics/bti56715998662PrimaryDenise Scholtensdscholtens@northwestern.eduPersonPrimary contactAPECSProteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.https://trac.nbic.nl/apecs/apecsbiotools:apecsCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3524Simulation experimentLinuxWindowsMacPythonProteomicshttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3627Mass spectra calibrationhttp://www.mybiosoftware.com/apecs-intensity-based-peptide-selection.htmlSoftware cataloguehttps://trac.nbic.nl/apecs/wiki#no1General10.1021/pr100694420836568http://www.nbic.nlPersonPrimary contactAPEXAbsolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool.http://sourceforge.net/projects/apexqpt/apexbiotools:apex1.1.0Desktop applicationhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0108Protein expressionLinuxWindowsMacJavaProteomicshttp://edamontology.org/operation_3637Spectral countinghttp://edamontology.org/operation_3630Protein quantitationhttp://edamontology.org/operation_2423Detectionhttp://www.mybiosoftware.com/apex-1-1-0-quantitative-proteomics-tool.htmlSoftware catalogue10.1038/nbt127017187058Primaryhttp://www.marcottelab.org/PersonPrimary contactArchCandyTool able to decode protein sequence motifs that have a potential to form amyloids.http://bioinfo.montp.cnrs.fr/?r=ArchCandyarchcandybiotools:archcandyDesktop applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3092Protein feature detectionhttp://www.mybiosoftware.com/archcandy-detect-regions-in-protein-sequences-that-have-a-potential-to-form-amyloids.htmlSoftware cataloguehttp://bioinfo.montp.cnrs.fr/?r=ArchCandy&p=homeGeneral10.1016/j.jalz.2014.06.00725150734Andrey V. KajavaAndrey.Kajava@crbm.cnrs.frhttp://bioinfo.montp.cnrs.fr/index.phpPersonPrimary contactArchiPThis tool detects architectures of all-β and α/β-classeshttp://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archiparchipbiotools:archipWeb applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMacProteomicshttp://edamontology.org/operation_0319Protein secondary structure assignmenthttp://www.mybiosoftware.com/archip-2-1-detecting-architectures-of-all-β-and-αβ-classes.htmlSoftware cataloguehttp://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip&page=help&data=alldocsGeneral10.1142/s021972001241003x22809339Evgeniy Aksianovevaksianov@gmail.comPersonPrimary contactArchKIThis tool performs a structural classification of kinase loops with information of functional residues to find relationships between structure and function of classified kinase-loops.http://bioinf.uab.es/cgi-bin/archki/loops.pl?class=all&set=ArchKIarchkibiotools:archkiWeb servicehttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0166Protein structural motifs and surfacesLinuxWindowsMacProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/archki-classification-common-functional-loops-kinase-super-families.htmlSoftware cataloguehttp://bioinf.uab.es/cgi-bin/archki/loops.pl?class=allGeneral10.1002/prot.2013615229886http://sbi.imim.es/cgi-bin/archdb/loops.pl?con=1PersonPrimary contactArShiftMethod of calculating side-chain aromatic chemical shifts from protein structures.http://www-sidechain.ch.cam.ac.uk/ArShift/arshiftbiotools:arshiftWeb applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3542Protein secondary structureLinuxWindowsMacRProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://www.mybiosoftware.com/arshift-structure-based-predictor-of-protein-aromatic-side-chain-proton-chemical-shifts.htmlSoftware cataloguehttp://www-sidechain.ch.cam.ac.uk/ArShift/GeneralDownloadable PDF within homepage.10.1002/anie.20110164121887824http://www-vendruscolo.ch.cam.ac.uk/index.htmlPersonPrimary contactASAPRatioStatistical analysis of protein ratios from ICAT, cICAT or SILAC experiments.http://tools.proteomecenter.org/ASAPRatio.phpasapratiobiotools:asapratioCommand-line toolDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityWindowsC++ms-utilsProteomicshttp://edamontology.org/operation_3638SILAChttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3741Differential protein expression analysishttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3705Isotope-coded protein labelhttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/operation_3632Isotopic distributions calculationhttp://edamontology.org/operation_3635Labeled quantificationhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXML

http://edamontology.org/data_1669P-valuehttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3655pepXML

http://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3655pepXML

http://ms-utils.orgSoftware cataloguehttp://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatioGeneral10.1021/ac034633i14640741Primarywebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorAtSubPA highly accurate subcellular localization prediction tool for annotating the Arabidopsis thaliana proteome.http://bioinfo3.noble.org/AtSubP/atsubpbiotools:atsubpWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0154Small moleculesLinuxWindowsMacProteomicshttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://bioinfo3.noble.org/AtSubP/?dowhat=HelpGeneral10.1104/pp.110.15685120647376AtSubP teambioinfo@noble.orgPersonPrimary contactAUTOHDAnalysis of H/D-exchange data using isotopic distributions.http://www.ms-utils.org/autohd.htmlautohdbiotools:autohdCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacCGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0404Protein hydrogen exchange rate calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2200FASTA-like (text)

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

http://ms-utils.orgSoftware cataloguehttp://www.ms-utils.org/autohd_download.htmlSource codehttp://www.ms-utils.org/autohd_download.htmlSource codehttp://www.ms-utils.org/autohd.htmlGeneral10.1016/s1044-0305(01)00301-411720389Magnus Palmbladmagnus.palmblad@gmail.comPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorBabelomicsIntegrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling. It integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods.http://babelomics.bioinfo.cipf.es/babelomicsbiotools:babelomics5Web applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3172MetabolomicsLinuxWindowsMacELIXIR-ESProteomicshttp://edamontology.org/operation_0277Pathway or network comparisonhttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3463Gene expression correlationhttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/operation_2495Gene expression analysishttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_3110Raw microarray datahttp://edamontology.org/data_2872ID listhttp://edamontology.org/data_2082Matrix

http://edamontology.org/data_0582Ontology

http://edamontology.org/data_1636Heat map

http://edamontology.org/data_2884Plot

https://github.com/babelomics/babelomicsRepositoryhttps://github.com/babelomics/babelomics/wiki#citationCitation instructionshttps://github.com/babelomics/babelomics/wikiGeneral10.1093/nar/gkv38425897133PMC4489263PrimaryComputational Genomics Department. Prince Felipe Research Center (CIPF)InstituteProviderhttp://bioinfo.cipf.esInstituteProvidercipf.esInstituteProviderbabelomics@cipf.es (Francisco García)babelomics@cipf.esPersonPrimary contactBAGEL3Automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases. Input is single or multiple FASTA formatted files.http://bagel.molgenrug.nlbagel3biotools:bagel3Web applicationhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacProteomicshttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3357Format detectionhttp://edamontology.org/operation_3643Tag-based peptide identificationhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_3767Protein identification10.1093/nar/gkt39123677608PMC3692055A.J. van Heela.j.van.heel@rug.nlPersonPrimary contactBetaVoidThis software recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area.http://voronoi.hanyang.ac.kr/software.htm#BetaVoidWinbetavoidbiotools:betavoidDesktop applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0121ProteomicsLinuxWindowsProteomicshttp://edamontology.org/operation_0245Protein structural motif recognitionhttp://www.mybiosoftware.com/betavoid-v1-molecular-voids-via-beta-complexes-and-voronoi-diagrams.htmlSoftware cataloguehttp://voronoi.hanyang.ac.kr/software.htm#BetaVoidWinGeneral10.1002/prot.2453724677176http://voronoi.hanyang.ac.kr/PersonPrimary contactBioDrugScreenResource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets are originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, created for this. This makes the resource highly valuable in drug discovery.http://www.biodrugscore.orgbiodrugscreenbiotools:biodrugscreenDatabase portalhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0209Medicinal chemistryhttp://edamontology.org/topic_2815Humanshttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3501Over-representation analysishttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_0482Protein-ligand docking10.1093/nar/gkp85219923229PMC2808957Samy O. Merouehsmeroueh@iupui.eduPersonPrimary contactBioLCCCAn analytic model of peptide retention.http://theorchromo.ru/biolcccbiotools:biolcccWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacms-utilsProteomicshttp://edamontology.org/operation_3633Retention time predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2979Peptide propertyhttp://edamontology.org/format_2331HTML

http://ms-utils.orgSoftware cataloguehttp://packages.python.org/pyteomics.biolccc/API/mespaceBioLCCC.htmlSource codehttp://theorchromo.ru/General10.1021/ac060913x17105170webmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorBiopLibLibrary of C routines for general programming and handling protein structurehttp://www.bioinf.org.uk/software/bioplib/index.htmlbioplibbiotools:bioplibCommand-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0166Protein structural motifs and surfacesLinuxWindowsMacCProteomicshttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/bioptools-1-1-a-set-of-command-line-tools-for-manipulating-protein-structure.htmlSoftware cataloguehttp://www.bioinf.org.uk/software/bioplib/bioplib/doc/html/pages.htmlGeneral10.1093/bioinformatics/btv48226323716PMC4673973Dr. Andrew C.R. Martinandrew@bioinf.org.ukhttp://www.bioinf.org.uk/PersonPrimary contactBioSunMSManagement of patients information and the analysis of peptide profiles from mass spectrometry.http://biosunms.sourceforge.net/biosunmsbiotools:biosunmsPlug-inhttp://edamontology.org/topic_0121ProteomicsGPL-1.0ProteomicsFree of chargehttp://edamontology.org/operation_3214Spectral analysishttps://sourceforge.net/projects/biosunms/files/latest/downloadBinarieshttps://sourceforge.net/p/biosunms/wiki/Home/General10.1186/1472-6947-9-1319220920PMC2654546Primarylabs.net@gmail.comPersonPrimary contactBioverseSystem that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.http://bioverse.compbio.washington.edu/bioversebiotools:bioverseWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksProteomicshttp://edamontology.org/operation_3455Molecular replacementhttp://edamontology.org/operation_3625Relation inference10.1093/nar/gkg55012824406PMC16895710.1093/bioinformatics/bti5141591972510.1093/nar/gki40115980482PMC116016210.1016/j.tibtech.2003.11.01014757037