PSI Mass Spectrometry Standards Working Group Summary

1. PSI Mass Spectrometry StandardsWorking Group Summary HUPO PSI MS Standards Working Group

2. PSI MSS & PI WGs Joint Session2:00 – 5:30 10 minutes each: • mzIdentML • mzQuantML (incl support for SRM) • mzTab (incl. support for SRM) • TraML • mzML & imzML & compression • metabolomics & ion mobility & SWATH-MS • PEFF • MIAPE: MS & MSI & Quant • Controlled vocabulary • Cross-linking • Protein grouping • PTM localization • RNA-seq assisted proteomics

3. TraML • Discussed ongoing implementation and use efforts • Identified some outdated information in documentation. TODO: update • Online validator has outdated CV. TODO: update • No schema or CV updates needed at this time • Discussed adding Waters format to jTraML converter

4. mzML • Schema remains stable with no needed changes • Many updates to the CV continue • imzML continues to be aligned with mzML • mz5 format was recently published as mzML clone using HDF5 not XML • Discussions ongoing by metabolomics groups about how mzML would meet the needs of the metabolomics community. Some terms already added. Expect some more proposals soon. • File size continues to be a significant problem…

5. mzML (or other) compression • Andy Dowsey & Faviel Gonzalez Galarza presented their work on compression • mz5 claims 50%+ space savings by using HDF5 • Implementation discussed vs. alternate HDF5 implementations • But significant space savings was achieved via tricks that could work in mzML • Discussed other work and proposed work in mass-spec aware compression • Possibility: alternative to zlib internal compression (currently supported) could be a mass-spec aware “mszip” compression scheme. Provided as a simple, open-source routine available in many languages • Possibility: Develop a variant of zlib that creates files that can be uncompressed normally, but allow indexing into the compressed file

6. File compression results Orbitrap profile-mode spectra ~50% compression using mz5 MB April 2013

7. Compressing mzML SYNAPT 57.1% 50.6% 45.1% 43.3% 36.8% April 2013

8. Other presentations • Shin presented on the use of RDF & TogoDB • Mathias presented about qcML

9. Ion mobility MS & SWATH-MS • Discussed with Waters their ion mobility data • Discussed required terms and practices for encoding raw IMS and peak-picked IMS data. Proposal to be publicized on lists for further comment • No schema change necessary

10. RNA-seq assisted proteomics • Good discussion of the state of the field on this workflow • Discussed using/promoting the PEFF format as a useful mechanism for encoding some of the RNA-seq results for use by proteomics searches • Discussed possible need to update MIAPE documents to capture information about what is done in this type of a workflow

11. Controlled Vocabulary • It is time to get the vendors to update their instrument and software terms again. Gerhard will repeat the effort done by Luisa years ago. • Worked to get rid of purgatory branch in CV • Discussed what to do with multiple SoftwareName:specificTerm entries that are effectively the same concept. Start by grouping similar terms under a common parent • Discussed constraining some terms with an is_a relationship to a concept like “value between 0 and 1 inclusive”

12. PEFF (PSI Extended Fasta Format) • Interest in finalising the format specification and makeitavailable • Cannotexpectthat (most of the) DB providers willproduceit in addition to theirexisting format • Cannotexpectthat (most of the) searchengineswillfullytakeadvantage of its structure (variants, PTMs, …) in the identification jobs • A converter(«source»-to-PEFF) and a readeralreadyexist . Couldbe a referenceimplementation =>A few minor open issues to beresolved and finalise the recommendation

13. MIAPE-MSI • Document isupdated • Mapping to mzIdentMLisvalidated • Collection of up-to-date example instance documents ongoing • Semanticvalidator for mzIdentMLongoing => Preparesubmission of version 1.2 to PSI doc process