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GET /api/t/?topic=%22Proteomics%22
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"http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3343", "term": "Compound libraries and screening" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/matchms/ms2deepscore", "type": [ "Repository" ], "note": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/recetox/suite_ms2deepscore/2b7360b26610", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore", "type": "Tool wrapper (Galaxy)", "note": null, "version": null }, { "url": "https://github.com/matchms/ms2deepscore", "type": "Source code", "note": null, "version": null }, { "url": "https://pypi.org/project/ms2deepscore/", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/2021.04.18.440324", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Florian Huber", "email": "f.huber@esciencecenter.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-3535-9406", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-10-11T08:42:43.272159Z", "lastUpdate": "2025-11-04T08:54:50.531589Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MAW", "description": "Metabolome Annotation Workflow for untargeted tandem mass spectrometry.", "homepage": "https://github.com/zmahnoor14/MAW", "biotoolsID": "maw", "biotoolsCURIE": "biotools:maw", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3643", "term": "Tag-based peptide identification" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/zmahnoor14/MAW-Benchmark", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00695-y", "pmid": "36871033", "pmcid": "PMC9985203", "type": [], "version": null, "note": null, "metadata": { "title": "MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry", "abstract": "Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC–MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub (https://github.com/zmahnoor14/MAW) The performance of MAW is evaluated on two case studies. MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.", "date": "2023-12-01T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Zulfiqar M." }, { "name": "Gadelha L." }, { "name": "Steinbeck C." }, { "name": "Sorokina M." }, { "name": "Peters K." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Mahnoor Zulfiqar", "email": "mahnoor.zulfiqar@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christoph Steinbeck", "email": "christoph.steinbeck@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Kristian Peters", "email": "kristian.peters@ipb-halle.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Luiz Gadelha", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Maria Sorokina", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-08-24T10:15:08.106111Z", "lastUpdate": "2025-11-03T16:47:22.668278Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "El-MAVEN", "description": "Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.", "homepage": "https://github.com/ElucidataInc/ElMaven", "biotoolsID": "El-MAVEN", "biotoolsCURIE": "biotools:El-MAVEN", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-11-03T16:47:19.388844Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSNovelist", "description": "De novo structure generation from mass spectra.", "homepage": "https://github.com/meowcat/MSNovelist", "biotoolsID": "msnovelist", "biotoolsCURIE": "biotools:msnovelist", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" } ], "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_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Java" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41592-022-01486-3", "pmid": "35637304", "pmcid": "PMC9262714", "type": [], "version": null, "note": null, "metadata": { "title": "MSNovelist: de novo structure generation from mass spectra", "abstract": "© 2022, The Author(s).Current methods for structure elucidation of small molecules rely on finding similarity with spectra of known compounds, but do not predict structures de novo for unknown compound classes. We present MSNovelist, which combines fingerprint prediction with an encoder–decoder neural network to generate structures de novo solely from tandem mass spectrometry (MS2) spectra. In an evaluation with 3,863 MS2 spectra from the Global Natural Product Social Molecular Networking site, MSNovelist predicted 25% of structures correctly on first rank, retrieved 45% of structures overall and reproduced 61% of correct database annotations, without having ever seen the structure in the training phase. Similarly, for the CASMI 2016 challenge, MSNovelist correctly predicted 26% and retrieved 57% of structures, recovering 64% of correct database annotations. Finally, we illustrate the application of MSNovelist in a bryophyte MS2 dataset, in which de novo structure prediction substantially outscored the best database candidate for seven spectra. MSNovelist is ideally suited to complement library-based annotation in the case of poorly represented analyte classes and novel compounds.", "date": "2022-07-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Stravs M.A." }, { "name": "Duhrkop K." }, { "name": "Bocker S." }, { "name": "Zamboni N." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Nicola Zamboni", "email": "zamboni@imsb.biol.ethz.ch", "url": null, "orcidid": "https://orcid.org/0000-0003-1271-1021", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9304-8091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Kai Dührkop", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9056-0540", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Michael A. Stravs", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1426-8572", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-05T21:19:03.847868Z", "lastUpdate": "2025-11-03T16:47:18.329938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "peakPantheR", "description": "R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets.", "homepage": "https://phenomecentre.github.io/peakPantheR.github.io/", "biotoolsID": "peakpanther", "biotoolsCURIE": "biotools:peakpanther", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bioconductor.org/packages/peakPantheR/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/phenomecentre/metabotyping-dementia-urine", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/phenomecentre/peakPantheR/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://phenomecentre.github.io/peakPantheR.github.io/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab433", "pmid": "34125879", "pmcid": "PMC8665750", "type": [], "version": null, "note": null, "metadata": { "title": "Extraction and integration of annotated metabolic features in LC-MS profiling datasets", "abstract": "Summary: Untargeted liquid chromatography-mass spectrometry (LC-MS) profiling assays are capable of measuring thousands of chemical compounds in a single sample, but unreliable feature extraction and metabolite identification remain considerable barriers to their interpretation and usefulness. peakPantheR (Peak Picking and ANnoTation of High-resolution Experiments in R) is an R package for the targeted extraction and integration of annotated features from LC-MS profiling experiments. It takes advantage of chromatographic and spectral databases and prior information of sample matrix composition to generate annotated and interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.", "date": "2021-12-15T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Wolfer A.M." }, { "name": "Correia G.D.S." }, { "name": "Sands C.J." }, { "name": "Camuzeaux S." }, { "name": "Yuen A.H.Y." }, { "name": "Chekmeneva E." }, { "name": "Takats Z." }, { "name": "Pearce J.T.M." }, { "name": "Lewis M.R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Arnaud M Wolfer", "email": "phenomecentre@imperial.ac.uk", "url": null, "orcidid": "https://orcid.org/0000-0001-5856-3218", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Goncalo Correia", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8271-9294", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jake Pearce", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Caroline Sands", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2021-10-28T20:02:19.622064Z", "lastUpdate": "2025-11-03T16:47:17.380949Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CANOPUS", "description": "CANOPUS is a tool for predicting compound classes directly from MS/MS. Because it does not depend on any database, CANOPUS is suitable for the classification of unknowns.", "homepage": "https://bio.informatik.uni-jena.de/software/canopus/", "biotoolsID": "canopus", "biotoolsCURIE": "biotools:canopus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/kaibioinfo/canopus_treemap", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41587-020-0740-8", "pmid": "33230292", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra", "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretation of experimental data. Here we describe CANOPUS (class assignment and ontology prediction using mass spectrometry), a computational tool for systematic compound class annotation. CANOPUS uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes. CANOPUS explicitly targets compounds for which neither spectral nor structural reference data are available and predicts classes lacking tandem mass spectrometry training data. In evaluation using reference data, CANOPUS reached very high prediction performance (average accuracy of 99.7% in cross-validation) and outperformed four baseline methods. We demonstrate the broad utility of CANOPUS by investigating the effect of microbial colonization in the mouse digestive system, through analysis of the chemodiversity of different Euphorbia plants and regarding the discovery of a marine natural product, revealing biological insights at the compound class level.", "date": "2021-04-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Duhrkop K." }, { "name": "Nothias L.-F." }, { "name": "Fleischauer M." }, { "name": "Reher R." }, { "name": "Ludwig M." }, { "name": "Hoffmann M.A." }, { "name": "Petras D." }, { "name": "Gerwick W.H." }, { "name": "Rousu J." }, { "name": "Dorrestein P.C." }, { "name": "Bocker S." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T11:58:45Z", "lastUpdate": "2025-11-03T16:47:13.400194Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PeakForest", "description": "A multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.", "homepage": "https://peakforest.org", "biotoolsID": "peakforest", "biotoolsCURIE": "biotools:peakforest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java", "JavaScript" ], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/peakforest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/S11306-022-01899-3", "pmid": "35699774", "pmcid": "PMC9197906", "type": [], "version": null, "note": null, "metadata": { "title": "PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management", "abstract": "© 2022, The Author(s).Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest.", "date": "2022-06-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Paulhe N." }, { "name": "Canlet C." }, { "name": "Damont A." }, { "name": "Peyriga L." }, { "name": "Durand S." }, { "name": "Deborde C." }, { "name": "Alves S." }, { "name": "Bernillon S." }, { "name": "Berton T." }, { "name": "Bir R." }, { "name": "Bouville A." }, { "name": "Cahoreau E." }, { "name": "Centeno D." }, { "name": "Costantino R." }, { "name": "Debrauwer L." }, { "name": "Delabriere A." }, { "name": "Duperier C." }, { "name": "Emery S." }, { "name": "Flandin A." }, { "name": "Hohenester U." }, { "name": "Jacob D." }, { "name": "Joly C." }, { "name": "Jousse C." }, { "name": "Lagree M." }, { "name": "Lamari N." }, { "name": "Lefebvre M." }, { "name": "Lopez-Piffet C." }, { "name": "Lyan B." }, { "name": "Maucourt M." }, { "name": "Migne C." }, { "name": "Olivier M.-F." }, { "name": "Rathahao-Paris E." }, { "name": "Petriacq P." }, { "name": "Pinelli J." }, { "name": "Roch L." }, { "name": "Roger P." }, { "name": "Roques S." }, { "name": "Tabet J.-C." }, { "name": "Tremblay-Franco M." }, { "name": "Traikia M." }, { "name": "Warnet A." }, { "name": "Zhendre V." }, { "name": "Rolin D." }, { "name": "Jourdan F." }, { "name": "Thevenot E." }, { "name": "Moing A." }, { "name": "Jamin E." }, { "name": "Fenaille F." }, { "name": "Junot C." }, { "name": "Pujos-Guillot E." }, { "name": "Giacomoni F." } ], "journal": "Metabolomics" } } ], "credit": [ { "name": "Franck Giacomoni", "email": "Franck.Giacomoni@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-6063-4214", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Estelle Pujos-Guillot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christophe Junot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "François Fenaille", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-04T23:10:37.868759Z", "lastUpdate": "2025-11-03T16:47:12.424836Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BUDDY", "description": "Open-source cheminformatic software platform developed for MS-based metabolomics research.", "homepage": "https://github.com/HuanLab/BUDDY", "biotoolsID": "buddy", "biotoolsCURIE": "biotools:buddy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" }, { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C#" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://philipbear.github.io/BUDDY_Metabolomics", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-023-01850-x", "pmid": "37055660", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "BUDDY: molecular formula discovery via bottom-up MS/MS interrogation", "abstract": "A substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics, and molecular formula annotation is the starting point for unraveling their chemical identities. Here we present bottom-up tandem MS (MS/MS) interrogation, a method for de novo formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking and offers false discovery rate estimation. Compared with the mathematically exhaustive formula enumeration, our approach shrinks the formula candidate space by 42.8% on average. Method benchmarking on annotation accuracy was systematically carried out on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 recurrent unidentified spectra, our approach confidently annotated >5,000 novel molecular formulae absent from chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global optimization to refine formula annotations while revealing peak interrelationships. This approach allowed the systematic annotation of 37 fatty acid amide molecules in human fecal data. All bioinformatics pipelines are available in a standalone software, BUDDY (https://github.com/HuanLab/BUDDY)", "date": "2023-06-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Xing S." }, { "name": "Shen S." }, { "name": "Xu B." }, { "name": "Li X." }, { "name": "Huan T." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Tao Huan", "email": "thuan@chem.ubc.ca", "url": null, "orcidid": "http://orcid.org/0000-0001-6295-2435", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-12-01T15:46:02.196263Z", "lastUpdate": "2025-11-03T16:45:48.375514Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MS-DIAL", "description": "MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters)", "homepage": "http://prime.psc.riken.jp/compms/msdial/main.html", "biotoolsID": "ms_dial", "biotoolsCURIE": "biotools:ms_dial", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3636", "term": "MRM/SRM" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial", "type": [ "General" ], "note": null }, { "url": "http://prime.psc.riken.jp/compms/msdial/faq.html", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41587-020-0531-2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A lipidome atlas in MS-DIAL 4", "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1–2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.", "date": "2020-10-01T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Tsugawa H." }, { "name": "Ikeda K." }, { "name": "Takahashi M." }, { "name": "Satoh A." }, { "name": "Mori Y." }, { "name": "Uchino H." }, { "name": "Okahashi N." }, { "name": "Yamada Y." }, { "name": "Tada I." }, { "name": "Bonini P." }, { "name": "Higashi Y." }, { "name": "Okazaki Y." }, { "name": "Zhou Z." }, { "name": "Zhu Z.-J." }, { "name": "Koelmel J." }, { "name": "Cajka T." }, { "name": "Fiehn O." }, { "name": "Saito K." }, { "name": "Arita M." }, { "name": "Arita M." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Makoto Arita", "email": "makoto.arita@riken.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Hiroshi Tsugawa", "email": "hiroshi.tsugawa@riken.jp", "url": null, "orcidid": "https://orcid.org/0000-0002-2015-3958", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:56:35Z", "lastUpdate": "2025-11-03T16:45:45.835795Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "tidyMass", "description": "An Object-oriented Reproducible Analysis Framework for LC-MS Data.", "homepage": "https://www.tidymass.org/", "biotoolsID": "tidymass", "biotoolsCURIE": "biotools:tidymass", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "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/tidymass", "type": [ "Repository" ], "note": null }, { "url": "https://tidymass.tidymass.org/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/jaspershen/tidymass-case-study", "type": "Container file", "note": null, "version": null }, { "url": "https://hub.docker.com/r/jaspershen/tidymass", "type": "Container file", "note": null, "version": null }, { "url": "https://www.tidymass.org/start/tidymass_docker/", "type": "Container file", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/s41467-022-32155-w", "pmid": "35902589", "pmcid": "PMC9334349", "type": [], "version": null, "note": null, "metadata": { "title": "TidyMass an object-oriented reproducible analysis framework for LC–MS data", "abstract": "Reproducibility, traceability, and transparency have been long-standing issues for metabolomics data analysis. Multiple tools have been developed, but limitations still exist. Here, we present the tidyMass project (https://www.tidymass.org/) a comprehensive R-based computational framework that can achieve the traceable, shareable, and reproducible workflow needs of data processing and analysis for LC-MS-based untargeted metabolomics. TidyMass is an ecosystem of R packages that share an underlying design philosophy, grammar, and data structure, which provides a comprehensive, reproducible, and object-oriented computational framework. The modular architecture makes tidyMass a highly flexible and extensible tool, which other users can improve and integrate with other tools to customize their own pipeline.", "date": "2022-12-01T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Shen X." }, { "name": "Yan H." }, { "name": "Wang C." }, { "name": "Gao P." }, { "name": "Johnson C.H." }, { "name": "Snyder M.P." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Caroline H. Johnson", "email": "caroline.johnson@yale.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Michael P. Snyder", "email": "mpsnyder@stanford.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaotao Shen", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-9608-9964", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Hong Yan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-11-25T21:43:37.501728Z", "lastUpdate": "2025-11-03T16:45:44.856713Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "GNPS", "description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.", "homepage": "https://gnps.ucsd.edu/", "biotoolsID": "gnps", "biotoolsCURIE": "biotools:gnps", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3637", "term": "Spectral counting" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [], "language": [], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://groups.google.com/forum/#!forum/molecular_networking_bug_reports", "type": [ "Discussion forum" ], "note": null } ], "download": [], "documentation": [ { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/", "type": [ "General" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/quickstart/", "type": [ "Quick start guide" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/api/", "type": [ "API documentation" ], "note": null }, { "url": "https://ccms-ucsd.github.io/GNPSDocumentation/faq/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/NBT.3597", "pmid": "27504778", "pmcid": "PMC5321674", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking", "abstract": "© 2016 Nature America, Inc. All rights reserved.The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu) an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.", "date": "2016-09-08T00:00:00Z", "citationCount": 1024, "authors": [ { "name": "Wang M." }, { "name": "Carver J.J." }, { "name": "Phelan V.V." }, { "name": "Sanchez L.M." }, { "name": "Garg N." }, { "name": "Peng Y." }, { "name": "Nguyen D.D." }, { "name": "Watrous J." }, { "name": "Kapono C.A." }, { "name": "Luzzatto-Knaan T." }, { "name": "Porto C." }, { "name": "Bouslimani A." }, { "name": "Melnik A.V." }, { "name": "Meehan M.J." }, { "name": "Liu W.-T." }, { "name": "Crusemann M." }, { "name": "Boudreau P.D." }, { "name": "Esquenazi E." }, { "name": "Sandoval-Calderon M." }, { "name": "Kersten R.D." }, { "name": "Pace L.A." }, { "name": "Quinn R.A." }, { "name": "Duncan K.R." }, { "name": "Hsu C.-C." }, { "name": "Floros D.J." }, { "name": "Gavilan R.G." }, { "name": "Kleigrewe K." }, { "name": "Northen T." }, { "name": "Dutton R.J." }, { "name": "Parrot D." }, { "name": "Carlson E.E." }, { "name": "Aigle B." }, { "name": "Michelsen C.F." }, { "name": "Jelsbak L." }, { "name": "Sohlenkamp C." }, { "name": "Pevzner P." }, { "name": "Edlund A." }, { "name": "McLean J." }, { "name": "Piel J." }, { "name": "Murphy B.T." }, { "name": "Gerwick L." }, { "name": "Liaw C.-C." }, { "name": "Yang Y.-L." }, { "name": "Humpf H.-U." }, { "name": "Maansson M." }, { "name": "Keyzers R.A." }, { "name": "Sims A.C." }, { "name": "Johnson A.R." }, { "name": "Sidebottom A.M." }, { "name": "Sedio B.E." }, { "name": "Klitgaard A." }, { "name": "Larson C.B." }, { "name": "Boya C.A.P." }, { "name": "Torres-Mendoza D." }, { "name": "Gonzalez D.J." }, { "name": "Silva D.B." }, { "name": "Marques L.M." }, { "name": "Demarque D.P." }, { "name": "Pociute E." }, { "name": "O'Neill E.C." }, { "name": "Briand E." }, { "name": "Helfrich E.J.N." }, { "name": "Granatosky E.A." }, { "name": "Glukhov E." }, { "name": "Ryffel F." }, { "name": "Houson H." }, { "name": "Mohimani H." }, { "name": "Kharbush J.J." }, { "name": "Zeng Y." }, { "name": "Vorholt J.A." }, { "name": "Kurita K.L." }, { "name": "Charusanti P." }, { "name": "McPhail K.L." }, { "name": "Nielsen K.F." }, { "name": "Vuong L." }, { "name": "Elfeki M." }, { "name": "Traxler M.F." }, { "name": "Engene N." }, { "name": "Koyama N." }, { "name": "Vining O.B." }, { "name": "Baric R." }, { "name": "Silva R.R." }, { "name": "Mascuch S.J." }, { "name": "Tomasi S." }, { "name": "Jenkins S." }, { "name": "Macherla V." }, { "name": "Hoffman T." }, { "name": "Agarwal V." }, { "name": "Williams P.G." }, { "name": "Dai J." }, { "name": "Neupane R." }, { "name": "Gurr J." }, { "name": "Rodriguez A.M.C." }, { "name": "Lamsa A." }, { "name": "Zhang C." }, { "name": "Dorrestein K." }, { "name": "Duggan B.M." }, { "name": "Almaliti J." }, { "name": "Allard P.-M." }, { "name": "Phapale P." }, { "name": "Nothias L.-F." }, { "name": "Alexandrov T." }, { "name": "Litaudon M." }, { "name": "Wolfender J.-L." }, { "name": "Kyle J.E." }, { "name": "Metz T.O." }, { "name": "Peryea T." }, { "name": "Nguyen D.-T." }, { "name": "VanLeer D." }, { "name": "Shinn P." }, { "name": "Jadhav A." }, { "name": "Muller R." }, { "name": "Waters K.M." }, { "name": "Shi W." }, { "name": "Liu X." }, { "name": "Zhang L." }, { "name": "Knight R." }, { "name": "Jensen P.R." }, { "name": "Palsson B.O." }, { "name": "Pogliano K." }, { "name": "Linington R.G." }, { "name": "Gutierrez M." }, { "name": "Lopes N.P." }, { "name": "Gerwick W.H." }, { "name": "Moore B.S." }, { "name": "Dorrestein P.C." }, { "name": "Bandeira N." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Mingxun Wang", "email": "miw023@ucsd.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:04:08Z", "lastUpdate": "2025-11-03T16:45:43.961672Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GLORYx", "description": "Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics.\n\nNew E-Resource for Drug Discovery.\n\nRegioselectivity prediction for phase 1 and phase 2 metabolism.", "homepage": "https://nerdd.zbh.uni-hamburg.de/", "biotoolsID": "gloryx", "biotoolsCURIE": "biotools:gloryx", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" }, { "uri": "http://edamontology.org/operation_3929", "term": "Metabolic pathway prediction" }, { "uri": "http://edamontology.org/operation_0417", "term": "PTM site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/acs.chemrestox.0c00224", "pmid": "32786543", "pmcid": "PMC7887798", "type": [], "version": null, "note": null, "metadata": { "title": "GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics", "abstract": "Predicting the structures of metabolites formed in humans can provide advantageous insights for the development of drugs and other compounds. Here we present GLORYx, which integrates machine learning-based site of metabolism (SoM) prediction with reaction rule sets to predict and rank the structures of metabolites that could potentially be formed by phase 1 and/or phase 2 metabolism. GLORYx extends the approach from our previously developed tool GLORY, which predicted metabolite structures for cytochrome P450-mediated metabolism only. A robust approach to ranking the predicted metabolites is attained by using the SoM probabilities predicted by the FAME 3 machine learning models to score the predicted metabolites. On a manually curated test data set containing both phase 1 and phase 2 metabolites, GLORYx achieves a recall of 77% and an area under the receiver operating characteristic curve (AUC) of 0.79. Separate analysis of performance on a large amount of freely available phase 1 and phase 2 metabolite data indicates that achieving a meaningful ranking of predicted metabolites is more difficult for phase 2 than for phase 1 metabolites. GLORYx is freely available as a web server at https://nerdd.zbh.uni-hamburg.de/ and is also provided as a software package upon request. The data sets as well as all the reaction rules from this work are also made freely available.", "date": "2021-02-15T00:00:00Z", "citationCount": 69, "authors": [ { "name": "De Bruyn Kops C." }, { "name": "Sicho M." }, { "name": "Mazzolari A." }, { "name": "Kirchmair J." } ], "journal": "Chemical Research in Toxicology" } } ], "credit": [], "owner": "Niclaskn", "additionDate": "2021-01-18T10:24:45Z", "lastUpdate": "2025-11-03T16:44:03.823692Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CliqueMS", "description": "Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.", "homepage": "https://github.com/osenan/cliqueMS", "biotoolsID": "CliqueMS", "biotoolsCURIE": "biotools:CliqueMS", "version": [ "0.3.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3798", "term": "Read binning" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/osenan/cliqueMS/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://cran.r-project.org/src/contrib/Archive/cliqueMS/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/osenan/cliqueMS/blob/master/vignettes/annotate_features.Rmd", "type": [ "Training material" ], "note": "Tutorial material" } ], "publication": [ { "doi": "10.1093/bioinformatics/btz207", "pmid": "30903689", "pmcid": "PMC6792096", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network", "abstract": "The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample.Results: Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generativemodel; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools.", "date": "2019-10-15T00:00:00Z", "citationCount": 48, "authors": [ { "name": "Senan O." }, { "name": "Aguilar-Mogas A." }, { "name": "Navarro M." }, { "name": "Capellades J." }, { "name": "Noon L." }, { "name": "Burks D." }, { "name": "Yanes O." }, { "name": "Guimera R." }, { "name": "Sales-Pardo M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Oriol Senan", "email": "oriol.senan@urv.cat", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Ruta", "additionDate": "2019-07-04T14:05:39Z", "lastUpdate": "2025-11-03T16:44:03.166147Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NeatMS", "description": "NeatMS is an open source python package for untargeted LCMS signal labelling and filtering. NeatMS enables automated filtering of false positive MS peaks reported by commonly used LCMS data processing pipelines. NeatMS relies on neural network based classification.", "homepage": "https://anaconda.org/bioconda/neatms", "biotoolsID": "neatms", "biotoolsCURIE": "biotools:neatms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bihealth/NeatMS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://neatms.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1021/ACS.ANALCHEM.1C02220", "pmid": "35290737", "pmcid": "PMC8969107", "type": [], "version": null, "note": null, "metadata": { "title": "Deep Learning-Assisted Peak Curation for Large-Scale LC-MS Metabolomics", "abstract": "© 2022 American Chemical Society. All rights reserved.Available automated methods for peak detection in untargeted metabolomics suffer from poor precision. We present NeatMS, which uses machine learning based on a convoluted neural network to reduce the number and fraction of false peaks. NeatMS comes with a pre-trained model representing expert knowledge in the differentiation of true chemical signal from noise. Furthermore, it provides all necessary functions to easily train new models or improve existing ones by transfer learning. Thus, the tool improves peak curation and contributes to the robust and scalable analysis of large-scale experiments. We show how to integrate it into different liquid chromatography-mass spectrometry (LC-MS) analysis workflows, quantify its performance, and compare it to various other approaches. NeatMS software is available as open source on github under permissive MIT license and is also provided as easy-to-install PyPi and Bioconda packages.", "date": "2022-03-29T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Gloaguen Y." }, { "name": "Kirwan J.A." }, { "name": "Beule D." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Dieter Beule", "email": "dieter.beule@bih-charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Yoann Gloaguen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0493-8592", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jennifer A. Kirwan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-07-06T15:00:55.171504Z", "lastUpdate": "2025-11-03T16:32:44.163513Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "UmetaFlow", "description": "Untargeted metabolomics workflow for high-throughput data processing and analysis.", "homepage": "https://github.com/biosustain/snakemake_UmetaFlow", "biotoolsID": "umetaflow", "biotoolsCURIE": "biotools:umetaflow", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/biosustain/pyOpenMS_UmetaFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00724-w", "pmid": "37173725", "pmcid": "PMC10176759", "type": [], "version": null, "note": null, "metadata": { "title": "UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis", "abstract": "Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC–MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. We anticipate that UmetaFlow will provide a useful platform for the interpretation of large metabolomics datasets. Graphical Abstract: [Figure not available: see fulltext.]", "date": "2023-12-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Kontou E.E." }, { "name": "Walter A." }, { "name": "Alka O." }, { "name": "Pfeuffer J." }, { "name": "Sachsenberg T." }, { "name": "Mohite O.S." }, { "name": "Nuhamunada M." }, { "name": "Kohlbacher O." }, { "name": "Weber T." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Tilmann Weber", "email": "tiwe@biosustain.dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-01-02T02:11:50.145026Z", "lastUpdate": "2025-11-03T16:16:27.787938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ThermoRawFileParser", "description": "Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML", "homepage": "https://github.com/compomics/ThermoRawFileParser", "biotoolsID": "ThermoRawFileParser", "biotoolsCURIE": "biotools:ThermoRawFileParser", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3712", "term": "Thermo RAW" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "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_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Java", "C#" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/compomics/ThermoRawFileParserGUI", "type": [ "Repository" ], "note": "ThermoRawFileParserGUI" } ], "download": [ { "url": "https://github.com/compomics/ThermoRawFileParser/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/622852", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Computational Omics and Systems Biology Group", "email": "compomics.list@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:10:29Z", "lastUpdate": "2025-11-03T16:16:26.016194Z", "editPermission": { "type": "group", "authors": [ "veits@bmb.sdu.dk", "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PeptideShaker", "description": "PeptideShaker 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. 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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. 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It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python. org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com [Figure not available: see fulltext.] © 2013 American Society for Mass Spectrometry.", "date": "2013-02-01T00:00:00Z", "citationCount": 141, "authors": [ { "name": "Goloborodko A.A." }, { "name": "Levitsky L.I." }, { "name": "Ivanov M.V." }, { "name": "Gorshkov M.V." } ], "journal": "Journal of the American Society for Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.8b00717", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework", "abstract": "Many of the novel ideas that drive today's proteomic technologies are focused essentially on experimental or data-processing workflows. The latter are implemented and published in a number of ways, from custom scripts and programs, to projects built using general-purpose or specialized workflow engines; a large part of routine data processing is performed manually or with custom scripts that remain unpublished. Facilitating the development of reproducible data-processing workflows becomes essential for increasing the efficiency of proteomic research. To assist in overcoming the bioinformatics challenges in the daily practice of proteomic laboratories, 5 years ago we developed and announced Pyteomics, a freely available open-source library providing Python interfaces to proteomic data. 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