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{ "name": "Comet", "description": "Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.", "homepage": "http://comet-ms.sourceforge.net/", "biotoolsID": "comet", "biotoolsCURIE": "biotools:comet", "version": [ "2016.01.2", "2023.01.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "Apache-2.0", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": "Source code", "note": null, "version": null }, { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://comet-ms.sourceforge.net/release/", "type": [ "Terms of use" ], "note": null }, { "url": "http://comet-ms.sourceforge.net/", "type": [ "Citation instructions", "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201200439", "pmid": "23148064", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Comet: An open-source MS/MS sequence database search tool", "abstract": "Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.", "date": "2013-01-01T00:00:00Z", "citationCount": 998, "authors": [ { "name": "Eng J.K." }, { "name": "Jahan T.A." }, { "name": "Hoopmann M.R." } ], "journal": "Proteomics" } }, { "doi": "10.1007/s13361-015-1179-x", "pmid": "26115965", "pmcid": "PMC4607604", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "A Deeper Look into Comet - Implementation and Features", "abstract": "The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington's academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these details in depth and highlight new features available in the latest release. Comet is freely available for download at http://comet-ms.sourceforge.net or it can be accessed as a component of a number of larger software projects into which it has been incorporated. (Figure Presented).", "date": "2015-11-01T00:00:00Z", "citationCount": 154, "authors": [ { "name": "Eng J.K." }, { "name": "Hoopmann M.R." }, { "name": "Jahan T.A." }, { "name": "Egertson J.D." }, { "name": "Noble W.S." }, { "name": "MacCoss M.J." } ], "journal": "Journal of the American Society for Mass Spectrometry" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Comet's Google group", "email": null, "url": "https://groups.google.com/forum/#!forum/comet-ms", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Comet's Google group", "email": null, "url": "https://groups.google.com/forum/#!forum/comet-ms", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2016-04-12T11:22:47Z", "lastUpdate": "2024-11-24T14:14:58.256477Z", "editPermission": { "type": "group", "authors": [ "n.m.palmblad@lumc.nl", "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }