Experiences to learn from the MS proteomics field
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The document discusses the development of data format standards for proteomics and mass spectrometry by Dr. Juan Antonio Vizcaíno at the 12th conference of the Metabolomics Society. It outlines current standards like mzML, mzIdentML, and mzQuantML, and emphasizes the importance of collaborative efforts within the community for data sharing and analysis. Additionally, tools and initiatives like the ProteoMX Consortium and the PRIDE Inspector are highlighted to facilitate data submission and visualization.
Experiences to learn from the MS proteomics field
- 1. Experiences to learn from the mass spectrometry proteomics field Dr. Juan Antonio Vizcaíno Proteomics Team Leader EMBL-EBI Hinxton, Cambridge, UK
- 2. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 •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 and now a new QC group. •Inter-group activities: MIAPE and Controlled Vocabularies. •Started in 2002, so some experience already… •One annual meeting in March-April, regular phone calls. •Peer Review for standards: PSI document process. http://www.psidev.info HUPO Proteomics Standards Initiative
- 3. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Current PSI Proteomics Standard File Formats for Mass Spectrometry • mzMLMS data • mzIdentMLIdentification • mzQuantMLQuantitation • mzTabFinal Results • TraMLSRM
- 4. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 • mzML is actively used already to store MS data (very flexible format). • mzTab is a tab-delimited format that it is being extended to support MS metabolomics data in a better way. It can be used for both identification and quantification results. • mzQuantML and TraML could be used with small molecule data, but it has not been tested. Reuse of data standards in metabolomics
- 5. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 • mzML is actively used already to store MS data (very flexible format). • mzTab is a tab-delimited format that it is being extended to support MS metabolomics data in a better way. It can be used for both identification and quantification results. • Meeting next week in Liverpool organised by A. Jones. • mzQuantML and TraML could be used with small molecule data, but it has not been tested. Reuse of data standards in metabolomics
- 6. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Current Standard File Formats that are or could be used in metabolomics • mzMLMS data • mzIdentMLIdentification • mzQuantML *Quantitation • mzTabFinal Results • TraML *SRM
- 7. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Current vision for data exchange standards in MS Neumann (IPB-Halle), Proteomics and HUPO-PSI community
- 8. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 imzML: data standard for mass imaging data http://www.imzml.org Not a PSI format: Based on mzML
- 9. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 qcML files to be generated after submission • XML format that captures output from QC pipelines
- 10. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 • Don’t reinvent the wheel! There is no need… • Software libraries (APIs) to handle the standards. • Data converters. • Data visualisation tools. • Data analysis tools and workflows. • A big proportion of the available software is open source. Opportunity to reuse and extend existing software
- 11. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 mzML: more software available The most popular search engines support mzML Many parser libraries available Conversion from raw files into mzMLhttp://www.psidev.info/mzml_1_0_0
- 12. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Data visualisation: PRIDE Inspector Toolsuite Wang et al., Nat. Biotechnology, 2012 Perez-Riverol et al., MCP, 2016 PRIDE Inspector Toolsuite PRIDE Inspector Toolsuite supports: - PRIDE XML - mzIdentML - mzML & all types of spectra files - mzTab identification and Quantification https://github.com/PRIDE-Toolsuite/
- 13. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 OpenMS/TOPP • OpenMS – an open-source C++ framework for computational mass spectrometry • Jointly developed at ETH Zürich, FU Berlin, University of Tübingen • Open source: BSD 3-clause license • Portable: available on Windows, OSX, and Linux • TOPP – The OpenMS Proteomics Pipeline • Building blocks: one application for each analysis step • All applications share identical user interfaces • Uses PSI standard formats and integrates seamlessly with other applications supporting these formats • Can be integrated in various workflow systems • TOPPAS – TOPP Pipeline Assistant • Galaxy • WS-PGRADE • KNIME Kohlbacher et al., Bioinformatics (2007), 23:e191
- 14. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 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), MassIVE (UCSD, San Diego) and jPOST (Japan) will be integrated in July 2016. • 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
- 15. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 PRIDE Archive submitted datasets up until 1st April, 2016 • In the last complete year: on average, >150 submitted datasets per month • Size of PRIDE Archive: ~ 220TB
- 16. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Vendor support for mzIdentML has grown in parallel with the number of submitted datasets 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-
- 17. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 •Develop tools in parallel with the data standards. •Don’t reinvent the wheel! Many ideas and software already there. •Ideally, get vendors involved as soon as possible. •Data repositories and data standards are a perfect match. Conclusions
- 18. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Acknowlegements and further reading… http://www.psidev.info Poster P18
- 19. Juan A. Vizcaíno juan@ebi.ac.uk 12th Conference of the Metabolomics Society Dublin, 27 June 2016 Questions?