Introduction to the PSI standard data formats
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This document provides an overview of proteomics data standards developed by the Proteomics Standards Initiative (PSI). It discusses the need for data standards, describes existing PSI standards like mzML for mass spectrometry data, mzIdentML for identification data, and mzTab for final results. The document also provides background on the development and adoption of these standards over time to support the evolving needs of the proteomics community.
Introduction to the PSI standard data formats
- 1. Introduction to the PSI standard data formats Dr. Juan Antonio Vizcaíno EMBL-EBI Hinxton, Cambridge, UK
- 2. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards
- 3. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Standards are needed in real life: also in bioinformatics… With a small number of standards, converters are feasible Data standards are needed
- 4. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Taken from Biocomicals, http://biocomicals.blogspot.com
- 5. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Mass Spectrometry (MS)-based proteomics • Many different workflows -> Many different data types -> Need for several data standards. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition (DDA) • Data independent acquisition (DIA) • Top down proteomics • Targeted mode: • SRM/MRM/PRM (Selected/ Multiple/Parallel Reaction Monitoring)
- 6. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards
- 7. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 •Develops data standards for proteomics. •Both data representation and annotation standards. •Involves data producers, database providers, software producers, publishers, everyone who wants to be involved… •Active Workgroups: MI, MS, PI, Mod and the new QC. •Inter-group activities: MIAPE and Controlled Vocabularies. •Started in 2002, so some experience already… •One annual meeting in March-April, regular phone calls. •Close interaction with the metabolomics community (MSI). http://www.psidev.info HUPO Proteomics Standards Initiative
- 8. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 PSI Deliverables •Minimum information (MIAPE) specifications: Format-independent specification of minimum information guidelines. •Formats: Usually XML-based (but also tab-delimited files), capable of representing the relevant Minimum Information, plus additional detailed data for the domain. •Controlled vocabularies: Usually an OBO-style hierarchical controlled vocabulary precisely defining the metadata that are encoded in the formats. •Databases and Tools: Foster open software implementations to make the standards truly useful. •Community interaction to ensure deposition of data in public repositories.
- 9. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 PSI MS Controlled Vocabulary Mayer et al., Database, 2013~2,700 terms by June 2017
- 10. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 The Ontology Lookup Service (OLS) http://www.ebi.ac.uk/ontology-lookup/
- 11. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards
- 12. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 The typical dilemma •Data standards need to be stable to promote adoption •Proteomics standards need to evolve very rapidly: • Data is inherently very complex • Experimental techniques are evolving all the time
- 13. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Current PSI Standard File Formats for MS • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 14. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Binary data mzData mzXML mzML XML-based files .dta, .pkl, .mgf, .ms2 Peak lists Data formats for mass spectra data
- 15. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 An example of success story: mzML • A data format for the storage and exchange of MS output files • Designed by merging the best aspects of both mzData and mzXML • Developed with full participation of academic researchers, hardware and software vendors • Expected to replace mzXML and mzData, but not expected to completely replace vendor binary formats • Captures spectra (raw data or peak lists), chromatograms and related metadata • Version 1.0 released in June 2008, v1.1 released in June 2009 • Many implementations already exist • Version 1.2 with enhanced compression considered for the near future. Martens et al., MCP, 2011
- 16. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 An example of success story: mzML The most popular search engines support mzML Many parser libraries available Conversion from raw files into mzMLhttp://www.psidev.info/mzml_1_0_0
- 17. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Current PSI Standard File Formats for MS • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 18. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzIdentML, mascot .dat, sequest .out, SpectrumMill .spo pep.xml, prot.xml Only qualitative data! Data formats for output from search engines
- 19. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzIdentML • XML-based data standard for peptide and protein identifications e.g. following database search and protein inference • Sections for all PSMs, proteins/protein groups, protocols/parameters etc. • Timeline: • Original 1.0 version in Aug 2009 • Version 1.1 stable (Aug 2011); Original manuscript published in MCP in 2012* • Well supported in lots of open source and commercial software • Fully supported by ProteomeXchange resources • 2012 onwards (mzIdentML 1.2): extended use cases • Better support for protein grouping. Manuscript published in Proteomics ** • 2017 mzIdentML 1.2 release; manuscript published at MCP*** * Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., et al., The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & Cellular Proteomics 2012, 11, M111.014381. ** Seymour, S. L., Farrah, T., Binz, P. A., Chalkley, R. J., et al., A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics 2014, 14, 2389-2399. *** Vizcaíno, J. A., Mayer G., Perkins S., Barsnes H., et al., The mzIdentML Data Standard Version 1.2, Supporting advances in Proteome Informatics. Molecular & Cellular Proteomics 2017, 16, 1275-1285.
- 20. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzIdentML 1.1 Data standard for peptide and protein identification data mzIdentML 1.2 2011- 2012 2017 New support for: - Cross-linking approaches - Peptide level scores - Modification localization scores - Proteogenomics approaches Improved support for: - Protein inference - Pre-fractionation - de novo sequencing - Spectral library searches Increasingly supported by the most- used proteomics software and databases jmzIdentML mzid Library ms-data-core-api MyriMatch ProteoAnnotator PIA ProCon
- 21. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Current PSI Standard File Formats for MS • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 22. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzQuantML status • XML-based standard for quantification data Can report tables of data (QuantLayers), columns are: StudyVariables, Assays or Ratios, rows are ProteinGroups, Proteins or Peptides • Can also capture 2D coordinates of quantified regions in LC-MS (Features) Timeline • Work started in Oct 2011, and progressed at various PSI meetings • Completed PSI process in Feb 2013 – version 1.0 release • Supports label-free (intensity), label-free (spectral counting), MS2 tag techniques (e.g. iTRAQ) and MS1 label techniques e.g. SILAC* • Updated in 2013-2014 to support SRM as a new technique**; mzqLibrary*** • 2015, mzQuantML 1.0.1 – minor update with SRM included Open issues • Not widely supported by software. No live development. Efforts are being put into mzTab support instead *Walzer et al. MCP 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506 **Qi et al. PROTEOMICS, 2015, 15(18):3152-62 *** Qi et al PROTEOMICS 2015, 15, 2592-2596.
- 23. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Current PSI Standard File Formats for MS • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 24. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzTab – Aims and concept • To provide a simple and efficient way of exchanging results from MS approaches. • Simpler summary report of the experimental results • Peptides and proteins identified in a given experimental setting • Small molecules identified • Reported quantification values • Technical and biological metadata • Easier to parse and use by the research community, systems biologists as well as providers of knowledge bases. • It can be used by non-experts in bioinformatics. • It does not aim to replace mzIdentMl and mzQuantML
- 25. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 mzTab - Sections • Basic information about experiment and sample • Key-Value pairsMetadata • Basic information about protein identifications • Table-basedProtein • Information about quantified peptides • Table-basedPeptide • Information about identified spectra • Table-basedPSM • Basic information about identified small molecules • Table-basedSmall Molecule Griss et al., MCP, 2014
- 26. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Metadata section - Example
- 27. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Current PSI Standard File Formats for MS • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 28. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Unify exchange of transitions with TraML • PSI’s TraML (Transitions Markup Language) • Format for encoding SRM/MRM transitions • Version 1.0.0 now released and published in MCP (Deutsch et al. 2012) Journal Articles Transitions Databases Excel sheets SRM Analysis Software Instruments TraML
- 29. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 PSI document process •Every data standard has to undergo a thorough review process… •In fact, in practice, two review processes happen in parallel: the PSI and manuscript review.
- 30. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Proteogenomics related data formats • Two ongoing formats are being developed: proBed (version 1 available) and proBAM (still under review). • Same overall objective: to map identified peptides to genome coordinates. • Different level of detail: • proBed is tab-delimited and simpler, based on the original BED format. Less level of detail. • proBAM is based in the original SAM/BAM formats, widely used in genomics. Much higher level of detail.
- 31. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Proteogenomics related data formats
- 32. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Provide your own data to genome browsers
- 33. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 TrackHubs in Genome Browsers
- 34. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Data standard publications mzML (for MS data) Martens et al., MCP, 2011 mzIdentML (peptide/protein IDs) Jones et al., MCP, 2012 Vizcaíno et al., MCP, 2017 TraML (for SRM transitions) Deutsch et al., MCP, 2012 mzQuantML (for quantitative data) Walzer et al., MCP, 2013 mzTab (ID and quantification) Griss et al., MCP, 2014 proBed & proBAM (proteogenomics) Menschaert et al., Genome Biology, 2018
- 35. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Importance of making software available jmzML (https://github.com/PRIDE-Utilities/jmzml) Cote et al., Proteomics, 2009 jmzIdentML (https://github.com/PRIDE-Utilities/jmzidentML) Reisinger et al., Proteomics, 2012 jmzReader (https://github.com/PRIDE-Utilities/jmzReader) Griss et al., Proteomics, 2012 jmzQuantML (https://github.com/UKQIDA/jmzquantml) Qi et al., Proteomics, 2014 jmzTab (https://github.com/PRIDE-Utilities/jmzTab) Xu et al., Proteomics, 2014 ms-data-core-api (https://github.com/PRIDE-Utilities/ms-data-core-api)Perez-Riverol et al., Bioinformatics, 2015 PSI promotes implementations. The reference libraries are always open source and can be used by anyone!
- 36. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 And also… protein-protein interactions PSI-XML: XML-based format • Version 2.5 is the working version • Version 3.0 under development MITAB: tab-delimited format
- 37. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Summary slide Deutsch et al., JPR, 2017
- 38. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018 Do you want to learn more?
- 39. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2018 Hinxton, 18 July 2018