Key points are not available for this paper at this time.
The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain. The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain. The Proteomics Standards Initiative (PSI) 1The abbreviations used are: APIapplication programming interfaceCSVcomma-separated valueCVcontrolled vocabularyemPAIexponentially modified Protein Abundance IndexFDRfalse discovery rateiPRGProteome Informatics Research GroupMIAPEMinimum Information about a Proteomics ExperimentMSmass spectrometryPDHprotein detection hypothesisPSIProteomics Standards InitiativePSMpeptide spectrum matchRGResearch GroupXMLExtensible Markup Language. 1The abbreviations used are: APIapplication programming interfaceCSVcomma-separated valueCVcontrolled vocabularyemPAIexponentially modified Protein Abundance IndexFDRfalse discovery rateiPRGProteome Informatics Research GroupMIAPEMinimum Information about a Proteomics ExperimentMSmass spectrometryPDHprotein detection hypothesisPSIProteomics Standards InitiativePSMpeptide spectrum matchRGResearch GroupXMLExtensible Markup Language. recently released the mzIdentML standard data format (stable version 1.1) for reporting peptide and protein identifications in order to improve capabilities for data sharing and make it simpler for bioinformatics groups to focus development on a single, comprehensive file format (1Jones A.R. Eisenacher M. Mayer G. Kohlbacher O. Siepen J. Hubbard S. Selley J. Searle B. Shofstahl J. Seymour S. Julian R. Binz P.-A. Deutsch E.W. Hermjakob H. Reisinger F. Griss J. Vizcaino J.A. Chambers M. Pizarro A. Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results.Mol. Cell. Proteomics. 2012; 11 (M111.014381)Abstract Full Text Full Text PDF PubMed Scopus (158) Google Scholar). The format is represented in XML and is formally defined by the combination of the XML Schema Definition and a separate mapping file describing where controlled vocabulary (CV) terms must be used within the format. A core part of the standard captures lists of peptide-spectrum matches (PSMs) with associated scores or measures, described by CV terms. Each PSM should be linked to the spectrum that was searched in a separate file, such as represented in the PSI's mzML standard (2Martens L. Chambers M. Sturm M. Kessner D. Levander F. Shofstahl J. Tang W.H. Römpp A. Neumann S. Pizarro A.D. Montecchi-Palazzi L. Tasman N. Coleman M. Reisinger F. Souda P. Hermjakob H. Binz P.-A. Deutsch E.W. mzML—a community standard for mass spectrometry data.Mol. Cell. Proteomics. 2011; 10 (R110.000133)Abstract Full Text Full Text PDF PubMed Scopus (452) Google Scholar). The PSM captures the modifications identified, again using CV terms sourced from Unimod (3Creasy D.M. Cottrell J.S. Unimod: protein modifications for mass spectrometry.Proteomics. 2004; 4: 1534-1536Crossref PubMed Scopus (239) Google Scholar) or the PSI-MOD ontology (4Montecchi-Palazzi L. Beavis R. Binz P.-A. Chalkley R.J. Cottrell J. Creasy D. Shofstahl J. Seymour S.L. Garavelli J.S. The PSI-MOD community standard for representation of protein modification data.Nat. Biotechnol. 2008; 26: 864-866Crossref PubMed Scopus (105) Google Scholar). In an mzIdentML file, each PSM is linked to all protein sequences from which the peptide could have been derived (using the enzyme specified in the search). The mzIdentML standard also has a separate section capturing protein identification results in a two-level hierarchy. The top level comprises groups of proteins representing a putatively detected “isoform”, with each group containing a list of individual proteins (entries in the database searched to be specific) for which there is ambiguity regarding which of those entities was actually identified, typically because of the existence of shared peptides (i.e. the well-known protein inference problem (5Nesvizhskii A.I. Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem.Mol. Cell. Proteomics. 2005; 4: 1419-1440Abstract Full Text Full Text PDF PubMed Scopus (791) Google Scholar)). Note that in this context an “isoform” is simply a group of accessions from the source database and could be the result of database errors (duplications, sequencing errors) as well as related biological entities. The format also contains structures for describing the search parameters in a standard way, sourcing CV terms from the PSI-MS CV for enzyme descriptors, score thresholds, and so on (6Mayer G. Montecchi-Palazzi L. Ovelleiro D. Jones A.R. Binz P.-A. Deutsch E.W. Chambers M. Kallhardt M. Levander F. Shofstahl J. Orchard S. Antonio Vizcaíno J. Hermjakob H. Stephan C. Meyer H.E. Eisenacher M. The HUPO proteomics standards initiative—mass spectrometry controlled vocabulary.Database (Oxford). 2013; 2013 (10.1093/database/bat009)Crossref PubMed Scopus (60) Google Scholar). application programming interface comma-separated value controlled vocabulary exponentially modified Protein Abundance Index false discovery rate Informatics Research Information about a Proteomics mass spectrometry protein detection Proteomics Standards Initiative peptide spectrum Research Markup Language. application programming interface comma-separated value controlled vocabulary exponentially modified Protein Abundance Index false discovery rate Informatics Research Information about a Proteomics mass spectrometry protein detection Proteomics Standards Initiative peptide spectrum Research Markup Language. The format contains some the of the source and tools are on users and there is support for mzIdentML from version Creasy D.M. Cottrell J.S. protein identification by using mass spectrometry PubMed Scopus Google a from the J. A. M. J. mass spectrometry data PubMed Scopus Google a for proteomic PubMed Scopus Google B. C. C. M. A. G. software for peptide sequencing by mass PubMed Scopus Google Chambers mass peptide identification by PubMed Scopus Google and the E.W. L. D. H. Tasman N. B. B. A.I. Aebersold R. A of the PubMed Scopus Google Scholar) D. Chambers M. R. D. P. source software for proteomics tools 2008; PubMed Scopus Google Scholar). In there is the for the and of mzIdentML in M. A. C. A. R. N. O. A. Kohlbacher O. open-source software for mass 2008; PubMed Scopus Google Scholar) and file format for within in the support other groups have a application programming interface for and mzIdentML F. R. F. D. Hermjakob H. Antonio Vizcaíno J. Jones A.R. a interface to the mzIdentML standard for peptide and protein identification 2012; PubMed Scopus Google Scholar). 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Julian Seymour S.L. for reporting the use of mass spectrometry in Biotechnol. 2008; 26: PubMed Scopus (60) Google Scholar). mzIdentML Informatics new CV terms to the PSI-MS new defined in a new mapping file, and some We have a of mzIdentML that semantic or on the all is mzIdentML be in The version of the mzidValidator be from the group standards by are represented in XML format. XML is by because it is an standard there are tools available for XML and the of the format be formally defined with an XML Schema Definition XML are not straightforward for to with and be by users tools. We have the ProteoIDViewer to users and with files in mzIdentML format. 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Ghali et al. (Sat,) studied this question.