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Proteomics data standards

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Juan Antonio Vizcaino

The document discusses data standards for proteomics, including those developed by the Proteomics Standards Initiative (PSI). It describes several existing PSI standards for mass spectrometry data, including mzML, mzIdentML, mzQuantML, and TraML. It provides an example of the successful mzML standard and discusses how mzIdentML has been widely adopted for representing peptide and protein identifications.

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Introduction to the PSI standard data formats Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Standards are needed in life: also in bioinformatics… With a small number of standards, data converters are feasible Data standards are needed
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Taken from Biocomical, http://biocomicals.blogspot.com
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 •Develops data format standards for proteomics. •Both data representation and annotation standards. •Involves data producers, database providers, software producers, publishers, … •Active Workgroups: MI, MS, PI, Mod. •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. http://www.psidev.info HUPO Proteomics Standards Initiative
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PSI Deliverables •Minimum information (MIAPE) specifications: Format-independent specification of minimum information guidelines. •Formats: Usually an XML schema (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 software implementations to make the standards truly useful. •Community interaction to ensure deposition of data in public repositories.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PSI MS Controlled Vocabulary Mayer et al., Database, 2013
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 •MS data: mzML (also used in MS metabolomics). •Protein and peptide identifications: mzIdentML. •Peptide and protein quantification: mzQuantML (also supports small molecules). •SRM transitions (for targeted proteomics): TraML. •Molecular interactions: PSI MI XML and MITAB. •Latest addition (just published): mzTab: identification and quantification results for peptides, proteins and small molecules (also used in MS metabolomics). www.psidev.info Existing data standards in proteomics
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Current PSI Standard File Formats for MS • mzTabFinal Results • TraMLSRM • mzQuantMLQuantitation • mzIdentMLIdentification • mzMLMS data
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Binary data mzData mzXML mzML XML-based files .dta, .pkl, .mgf, .ms2 Peak lists Data formats for mass spectra data
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 2014 Martens et al., MCP, 2011
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 An example of success story: mzML Martens et al., MCP, 2011
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Application of mzML to metabolomics
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML, mascot .dat, sequest .out, SpectrumMill .spo pep.xml, prot.xml Only qualitative data! Data formats for output from search engines
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML: peptide and protein identifications • Overview • XML-based data standard for peptide and protein identifications e.g. following database search and protein inference. • Sections for all PSMs, proteins/protein groups inferred, protocols/parameters etc. • Timeline: • Original 1.0 version in Aug 2009. • Version 1.1 stable (Aug 2011). • Manuscript published in MCP in 2012*. • 2012-2015: • Improving support for protein grouping multiple search engines, pre-fractionation approaches and de novo sequencing. • Now firmly embedded as part of ProteomeXchange submission process, and supported by lots of external software. * 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.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML: peptide and protein identifications * 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. MzIdentML CvList AnalysisSoftwareList AnalysisSampleCollection SequenceCollection AnalysisCollection AnalysisProtocolCollection DataCollection URLsof controlledvocabularies usedwithinthe file Softwarepackagesused Biologicalsamples analysed, annotated with CV terms Databaseentriesofprotein/ peptide sequencesidentifiedandmodifications Applicationofprotocol inputs= externalspectra1..n output= SpectrumIdentificationList1 SpectrumIdentificationProtocol ProteinDetectionProtocol SpectrumIdentificationProtocol AdditionalSearchParams ModificationParams Enzymes DatabaseFilters Parametersfor theprotein detection procedure Inputs AnalysisData AnalysisData SpectrumIdentificationList Thedatabasesearched and theinput fileconverted tomzIdentML SpectrumIdentificationResult SpectrumIdentificationItem ProteinDetectionList ProteinAmbiguityGroup ProteinDetectionHypothesis All identificationsmade from searchingonespectrum One(poly)peptide- spectrummatch Aset ofrelatedprotein identificationse.g.conflicting peptide-proteinassignments Asingle proteinidentification SpectrumIdentification ProteinDetectionApplicationofprotocol inputs= SpectrumIdentificationList1..n output= ProteinDetectionList1
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 An example: XML snippet of mzIdentML
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Support for mzIdentML Search Engine Results + MS files Search engines mzIdentML - Mascot - MSGF+ - Myrimatch and related tools from D. Tabb’s lab - OpenMS - PEAKS - PeptideShaker (several open source tools) - ProCon (ProteomeDiscoverer, Sequest) - Scaffold - TPP via the idConvert tool (ProteoWizard) - ProteinPilot (from version 5.0) - X!Tandem (from PILEDRIVER version) - Others: library for X!Tandem conversion, lab internal pipelines, … - Crux An increasing number of tools support export to mzIdentML 1.1 Updated list: http://www.psidev.info/tools-implementing-
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML status • Current status of mzIdentML 1.2 • Improved support for protein grouping** • Support for PTM localisation scoring added - COMPLETE • Support for peptide-level statistics added - COMPLETE • Better support for multiple search approaches - COMPLETE • Support for crosslinking approaches – INCOMPLETE • mzIdentML 1.2 submission to document process - INCOMPLETE ** 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.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML: Standard for quantitative data Overview • XML-based standard for quantification data – following use of quant software • 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 • Version 1.0 rc-1 submitted to the PSI process October 2011; Version 1.0 rc-2 June 2012; Re- submitted to PSI process in October 2012 • 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 • Schema is fixed with each technique defined by separate semantic rules, implemented in validator software • Manuscript published in MCP in summer 2013* • Updated in 2013-2014 to support SRM as a new technique** (version 1.0.1 just submitted to the document process). *Walzer et al. MCP 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506 **Qi et al. PROTEOMICS, 2015
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML: Standard for quantitative data *Walzer et al. MCP 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506 **Qi et al. PROTEOMICS, 2015
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML status Open issues • Updated in 2014 to support absolute quant techniques but not yet added to specification document • Some supporting software but not currently implemented for import in databases (PRIDE?). • No webpage for software implementations.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Wide variety of quantification techniques
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQ library • The “mzqLibrary” includes a set of applications/modules to facilitate the use of mzQuantML within analysis pipelines. • The “mzqLibrary” provides common routines for post- processing quantitative proteomics data via the command line interface or graphical user interface - called the “mzqViewer". • The mzqViewer integrates with R to produce a heat map or principal component analysis (PCA) on selected data tables. Line plots can also be produced showing peptide and protein quant data across MS runs. * Qi et al., Proteomics, 2015
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 The mzqLibrary can convert output of Progenesis (*.csv files), MaxQuant (*.txt files), and OpenMS (*.consensusXML files) into mzQuantML (*.mzq). The mzqLibrary can convert mzQuantML file to four file formats (XLS, CSV, HTML, and mzTab). mzqLibrary: Converter & Exporter
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 The last addition: 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Metadata section - Example
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Protein Section (label-free)
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzTab – Current implementations • jmzTab (Java API): Version 3.0 is now a stable version. Manuscript published in the journal Proteomics. • mzTab Validator, PRIDE XML to mzTab converter (PRIDE team). • mzIdentML and mzQuantML to mzTab converters (Andy Jones group). • Mascot (Matrix Science) exporter. • MaxQuant: exporter in beta is available. • OpenMS (version 1.10). • R/Bioconductor package Msnbase (L. Gatto, Cambridge University). • LipidDataAnalyzer (J. Hartler, University of Graz, see next talk). • Metabolights (EBI).
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzTab – ongoing development in metabolomics • More detailed modelling of MS metabolomics data • Led by S. Neumann (COSMOS EU FP7 project). • Extension from one to three sections. Example file exists at https://github.com/sneumann/mtbls2/faahKO.mzTab http://www.cosmos-fp7.eu/
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Unify exchange of transitions with TraML Deutsch et al., MCP, 2012
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Java library for working with TraML files It aims: - command line & simple GUI - TraML to TSV <-> TSV to TraML - TSV vendor formats from TSQ, QTRAP5500, AgilentQQQ Published: Helsens et al., JPR, 2011 TraML software implementations
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Data standard publications mzML (data standard for MS data) Martens et al., MCP, 2011 mzIdentML (standard for peptide/protein IDs) Jones et al., MCP, 2012 TraML (for SRM transitions) Deutsch et al., MCP, 2012 mzQuantML (for quantitative data) Waltzer et al., MCP, 2013 mzTab (peptide/protein ID and quantification) Griss et al., MCP, 2014 Some updates already going on (e.g. mzIdentML 1.2)
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Importance of making software available jmzML (http://code.google.com/p/jmzml/) Cote et al., Proteomics, 2009 jmzIdentML (http://code.google.com/p/jmzidentml/) Reisinger et al., Proteomics, 2012 jmzReader (http://code.google.com/p/jmzreader/) Griss et al., Proteomics, 2012 jmzQuantML (http://code.google.com/p/jmzquantml/) Qi et al., Proteomics, 2014 jmzTab (http://code.google.com/p/mztab/) Xu et al., Proteomics, 2014 PSI promotes implementations. The reference libraries are always open source.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeXchange Consortium • Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. • Includes PeptideAtlas (ISB, Seattle), PRIDE (Cambridge, UK) and (very recently) MassIVE (UCSD, San Diego). • EU FP7 CA (01/2011-> 06/2014). • Common identifier space (PXD identifiers) • Two supported data workflows: MS/MS and SRM. • Main objective: Make life easier for researchers http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 MBInfo The IMEx Consortium (www.imexconsortium.org) Orchard et al., Nat Methods, 2012
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Conclusions • The PSI is a very active group. • Big variety of data types in proteomics -> Several data standards available. • Adoption of standards (as usual) takes some time. • Public databases greatly benefit from them.
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Next meeting in Ghent on April!
Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Questions?

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Proteomics data standards

  • 1. Introduction to the PSI standard data formats Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator Proteomics Services Team EMBL-EBI Hinxton, Cambridge, UK
  • 2. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
  • 3. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
  • 4. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Standards are needed in life: also in bioinformatics… With a small number of standards, data converters are feasible Data standards are needed
  • 5. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Taken from Biocomical, http://biocomicals.blogspot.com
  • 6. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 • Data independent acquisition • Top down proteomics • Targeted mode: • SRM (Selected Reaction Monitoring)
  • 7. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
  • 8. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 •Develops data format standards for proteomics. •Both data representation and annotation standards. •Involves data producers, database providers, software producers, publishers, … •Active Workgroups: MI, MS, PI, Mod. •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. http://www.psidev.info HUPO Proteomics Standards Initiative
  • 9. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PSI Deliverables •Minimum information (MIAPE) specifications: Format-independent specification of minimum information guidelines. •Formats: Usually an XML schema (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 software implementations to make the standards truly useful. •Community interaction to ensure deposition of data in public repositories.
  • 10. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 PSI MS Controlled Vocabulary Mayer et al., Database, 2013
  • 11. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
  • 12. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 2015 Hinxton, 10 December 2015 •MS data: mzML (also used in MS metabolomics). •Protein and peptide identifications: mzIdentML. •Peptide and protein quantification: mzQuantML (also supports small molecules). •SRM transitions (for targeted proteomics): TraML. •Molecular interactions: PSI MI XML and MITAB. •Latest addition (just published): mzTab: identification and quantification results for peptides, proteins and small molecules (also used in MS metabolomics). www.psidev.info Existing data standards in proteomics
  • 14. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Current PSI Standard File Formats for MS • mzTabFinal Results • TraMLSRM • mzQuantMLQuantitation • mzIdentMLIdentification • mzMLMS data
  • 15. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Binary data mzData mzXML mzML XML-based files .dta, .pkl, .mgf, .ms2 Peak lists Data formats for mass spectra data
  • 16. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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 2014 Martens et al., MCP, 2011
  • 17. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 An example of success story: mzML Martens et al., MCP, 2011
  • 18. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 19. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Application of mzML to metabolomics
  • 20. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML, mascot .dat, sequest .out, SpectrumMill .spo pep.xml, prot.xml Only qualitative data! Data formats for output from search engines
  • 21. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML: peptide and protein identifications • Overview • XML-based data standard for peptide and protein identifications e.g. following database search and protein inference. • Sections for all PSMs, proteins/protein groups inferred, protocols/parameters etc. • Timeline: • Original 1.0 version in Aug 2009. • Version 1.1 stable (Aug 2011). • Manuscript published in MCP in 2012*. • 2012-2015: • Improving support for protein grouping multiple search engines, pre-fractionation approaches and de novo sequencing. • Now firmly embedded as part of ProteomeXchange submission process, and supported by lots of external software. * 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.
  • 22. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML: peptide and protein identifications * 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. MzIdentML CvList AnalysisSoftwareList AnalysisSampleCollection SequenceCollection AnalysisCollection AnalysisProtocolCollection DataCollection URLsof controlledvocabularies usedwithinthe file Softwarepackagesused Biologicalsamples analysed, annotated with CV terms Databaseentriesofprotein/ peptide sequencesidentifiedandmodifications Applicationofprotocol inputs= externalspectra1..n output= SpectrumIdentificationList1 SpectrumIdentificationProtocol ProteinDetectionProtocol SpectrumIdentificationProtocol AdditionalSearchParams ModificationParams Enzymes DatabaseFilters Parametersfor theprotein detection procedure Inputs AnalysisData AnalysisData SpectrumIdentificationList Thedatabasesearched and theinput fileconverted tomzIdentML SpectrumIdentificationResult SpectrumIdentificationItem ProteinDetectionList ProteinAmbiguityGroup ProteinDetectionHypothesis All identificationsmade from searchingonespectrum One(poly)peptide- spectrummatch Aset ofrelatedprotein identificationse.g.conflicting peptide-proteinassignments Asingle proteinidentification SpectrumIdentification ProteinDetectionApplicationofprotocol inputs= SpectrumIdentificationList1..n output= ProteinDetectionList1
  • 23. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 An example: XML snippet of mzIdentML
  • 24. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Support for mzIdentML Search Engine Results + MS files Search engines mzIdentML - Mascot - MSGF+ - Myrimatch and related tools from D. Tabb’s lab - OpenMS - PEAKS - PeptideShaker (several open source tools) - ProCon (ProteomeDiscoverer, Sequest) - Scaffold - TPP via the idConvert tool (ProteoWizard) - ProteinPilot (from version 5.0) - X!Tandem (from PILEDRIVER version) - Others: library for X!Tandem conversion, lab internal pipelines, … - Crux An increasing number of tools support export to mzIdentML 1.1 Updated list: http://www.psidev.info/tools-implementing-
  • 25. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzIdentML status • Current status of mzIdentML 1.2 • Improved support for protein grouping** • Support for PTM localisation scoring added - COMPLETE • Support for peptide-level statistics added - COMPLETE • Better support for multiple search approaches - COMPLETE • Support for crosslinking approaches – INCOMPLETE • mzIdentML 1.2 submission to document process - INCOMPLETE ** 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.
  • 26. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML: Standard for quantitative data Overview • XML-based standard for quantification data – following use of quant software • 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 • Version 1.0 rc-1 submitted to the PSI process October 2011; Version 1.0 rc-2 June 2012; Re- submitted to PSI process in October 2012 • 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 • Schema is fixed with each technique defined by separate semantic rules, implemented in validator software • Manuscript published in MCP in summer 2013* • Updated in 2013-2014 to support SRM as a new technique** (version 1.0.1 just submitted to the document process). *Walzer et al. MCP 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506 **Qi et al. PROTEOMICS, 2015
  • 27. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML: Standard for quantitative data *Walzer et al. MCP 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506 **Qi et al. PROTEOMICS, 2015
  • 28. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQuantML status Open issues • Updated in 2014 to support absolute quant techniques but not yet added to specification document • Some supporting software but not currently implemented for import in databases (PRIDE?). • No webpage for software implementations.
  • 29. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Wide variety of quantification techniques
  • 30. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzQ library • The “mzqLibrary” includes a set of applications/modules to facilitate the use of mzQuantML within analysis pipelines. • The “mzqLibrary” provides common routines for post- processing quantitative proteomics data via the command line interface or graphical user interface - called the “mzqViewer". • The mzqViewer integrates with R to produce a heat map or principal component analysis (PCA) on selected data tables. Line plots can also be produced showing peptide and protein quant data across MS runs. * Qi et al., Proteomics, 2015
  • 31. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 The mzqLibrary can convert output of Progenesis (*.csv files), MaxQuant (*.txt files), and OpenMS (*.consensusXML files) into mzQuantML (*.mzq). The mzqLibrary can convert mzQuantML file to four file formats (XLS, CSV, HTML, and mzTab). mzqLibrary: Converter & Exporter
  • 32. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 The last addition: 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
  • 33. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 34. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Metadata section - Example
  • 35. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Protein Section (label-free)
  • 36. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzTab – Current implementations • jmzTab (Java API): Version 3.0 is now a stable version. Manuscript published in the journal Proteomics. • mzTab Validator, PRIDE XML to mzTab converter (PRIDE team). • mzIdentML and mzQuantML to mzTab converters (Andy Jones group). • Mascot (Matrix Science) exporter. • MaxQuant: exporter in beta is available. • OpenMS (version 1.10). • R/Bioconductor package Msnbase (L. Gatto, Cambridge University). • LipidDataAnalyzer (J. Hartler, University of Graz, see next talk). • Metabolights (EBI).
  • 37. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 mzTab – ongoing development in metabolomics • More detailed modelling of MS metabolomics data • Led by S. Neumann (COSMOS EU FP7 project). • Extension from one to three sections. Example file exists at https://github.com/sneumann/mtbls2/faahKO.mzTab http://www.cosmos-fp7.eu/
  • 38. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 39. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Unify exchange of transitions with TraML Deutsch et al., MCP, 2012
  • 40. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Java library for working with TraML files It aims: - command line & simple GUI - TraML to TSV <-> TSV to TraML - TSV vendor formats from TSQ, QTRAP5500, AgilentQQQ Published: Helsens et al., JPR, 2011 TraML software implementations
  • 41. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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.
  • 42. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Data standard publications mzML (data standard for MS data) Martens et al., MCP, 2011 mzIdentML (standard for peptide/protein IDs) Jones et al., MCP, 2012 TraML (for SRM transitions) Deutsch et al., MCP, 2012 mzQuantML (for quantitative data) Waltzer et al., MCP, 2013 mzTab (peptide/protein ID and quantification) Griss et al., MCP, 2014 Some updates already going on (e.g. mzIdentML 1.2)
  • 43. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Importance of making software available jmzML (http://code.google.com/p/jmzml/) Cote et al., Proteomics, 2009 jmzIdentML (http://code.google.com/p/jmzidentml/) Reisinger et al., Proteomics, 2012 jmzReader (http://code.google.com/p/jmzreader/) Griss et al., Proteomics, 2012 jmzQuantML (http://code.google.com/p/jmzquantml/) Qi et al., Proteomics, 2014 jmzTab (http://code.google.com/p/mztab/) Xu et al., Proteomics, 2014 PSI promotes implementations. The reference libraries are always open source.
  • 44. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 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
  • 45. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Overview • A couple of slides about the need of data standards • The Proteomics Standards Initiative • Existing data standards • Connection with ProteomeXchange and IMEx
  • 46. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 ProteomeXchange Consortium • Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. • Includes PeptideAtlas (ISB, Seattle), PRIDE (Cambridge, UK) and (very recently) MassIVE (UCSD, San Diego). • EU FP7 CA (01/2011-> 06/2014). • Common identifier space (PXD identifiers) • Two supported data workflows: MS/MS and SRM. • Main objective: Make life easier for researchers http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014
  • 47. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 MBInfo The IMEx Consortium (www.imexconsortium.org) Orchard et al., Nat Methods, 2012
  • 48. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Conclusions • The PSI is a very active group. • Big variety of data types in proteomics -> Several data standards available. • Adoption of standards (as usual) takes some time. • Public databases greatly benefit from them.
  • 49. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Next meeting in Ghent on April!
  • 50. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2015 Hinxton, 10 December 2015 Questions?