PSI Mass Spectrometry StandardsWorking Group Summary

HUPO PSI MS Standards Working Group

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

2

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• Identified some outdated information in documentation.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• Online validator has outdated CV.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

3

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…

4

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

5

MB

April 2013

~50% compression using mz5

File compression results

Orbitrap profile-mode spectra

Compressing mzML

April 2013

SYNAPT

57.1%50.6%

36.8%

45.1% 43.3%

Other presentations

• Shin presented on the use of RDF & TogoDB

• Mathias presented about qcML

8

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

9

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

10

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”

11

• Interest in finalising the format specification and make it available

• Cannot expect that (most of the) DB providers will produce it in addition to their existing format

• Cannot expect that (most of the) search engines will fully take advantage of its structure (variants, PTMs, …) in the identification jobs

• A converter («source»-to-PEFF) and a reader already exist . Could be a reference implementation

=>A few minor open issues to be resolved and finalise the recommendation

PEFF (PSI Extended Fasta Format)

MIAPE-MSI

• Document is updated• Mapping to mzIdentML is validated

• Collection of up-to-date example instance documents ongoing

• Semantic validator for mzIdentML ongoing

=> Prepare submission of version 1.2 to PSI doc process