The Proteomics Standards Initiative (PSI)

The Proteomics Standards Initiative (PSI)

Dr. Juan Antonio Vizcaíno

Proteomics Team Leaderco-Chair PSI Proteomics Informatics Working Group

EMBL-European Bioinformatics Institute (EMBL-EBI)Hinxton, Cambridge, UK

Juan A. Vizcaí[email protected]

SmartLab Exchange Europe 2017Berlin, 8 February 2017

Data resources at EMBL-EBIGenes, genomes & variation

ArrayExpressExpression Atlas PRIDE

InterPro Pfam UniProt

ChEMBL ChEBI

Molecular structuresProtein Data Bank in EuropeElectron Microscopy Data Bank

European Nucleotide ArchiveEuropean Variation ArchiveEuropean Genome-phenome Archive

Gene & protein expression

Protein sequences, families & motifs

Chemical biologyReactions, interactions & pathways

IntActReactome

MetaboLights

SystemsBioModels Enzyme Portal BioSamples

Ensembl Ensembl Genomes

GWAS CatalogMetagenomics portal

Europe PubMed CentralGene OntologyExperimental Factor Ontology

Literature & ontologies



•Develops data format standards for proteomics.•Both data representation and annotation standards.•Involves data producers, database providers, software producers, publishers, … as many interested parties as possible.

•Started in 2002, so some experience already…•One annual meeting in March-April, regular phone calls.

http://www.psidev.info

HUPO Proteomics Standards Initiative

http://www.psidev.info/



PSI Deliverables

•Formats: Usually an XML schema (but also tab-delimited files)

•Controlled vocabularies: Usually an OBO-style hierarchical controlled vocabulary precisely defining the metadata that are encoded in the formats.

•Minimum information (MIAPE) specifications: Format-independent specification of minimum information guidelines.

•Databases and Tools: Foster software implementations to make the standards truly useful.

•Community interaction to ensure deposition of data in public repositories.



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 (Selected Reaction Monitoring)



Current PSI Standard File Formats for MS

• mzMLMS data

• mzIdentMLIdentification

• mzQuantMLQuantitation

• mzTabFinal Results

• TraMLSRM



Current PSI Standard File Formats for MS

• mzMLMS data

• mzIdentMLIdentification

• mzQuantMLQuantitation

• mzTabFinal Results

• TraMLSRM



Binary data

mzData

mzXMLmzML

XML-basedfiles

.dta, .pkl, .mgf,

.ms2Peak lists

Data formats for mass spectra data



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 usually a manuscript review as well.

Juan A. Vizcaíno

This slide could be deleted



PSI MS Controlled Vocabulary

Mayer et al., Database, 2013~2,600 terms by February 2017



Objectives of the PSI in the next 5 years• Improve adoption/support, especially in vendors

software

• Extend current proteomics data standards to MS metabolomics

• Facilitate reproducible analysis pipelines.

• Finalize compatible formats with genomics data e.g. proBed & proBAM (applicable for proteogenomics studies)

• Start working with the structural biology community (since MS proteomics is being increasingly used in that context)



HUPO Proteomics Standards Initiative (PSI)Lennart Martens (U Ghent)Darren Kessner (CSHS)Matt Chambers (Vanderbilt)Jim Shofstahl (Thermo)Fredrik Levander (U Lund)Steffen Neumann (IPB Halle)Juan Antonio Vizcaíno (EBI)Florian Reisinger (EBI)Luisa Montecchi-Palazzi (EBI)Randy Julian (Indigo)Natalie Tasman (Insilicos)Jari Häkkinen (U Lund)Brian Pratt (Insilicos)Erik Nilsson (Insilicos)Mike Coleman (Stowers)Luis Mendoza (ISB)David Shteynberg (ISB)Lars Nilse (Manchester)

David Tabb (Stellenbosch U)Mathias Walzer (U Tübingen)Gerben Menschaert (U Gent)Xiaojing Wang (Baylor)Chris Taylor (EBI)Patrick Pedrioli (ETHZ)Sean Seymour (AB Sciex)David Creasy (Matrix Science)Angel Pizarro (U Penn)Phil Jones (EBI)Jimmy Eng (U Washington)Kent Laursen (Indigo)Howard Read (Waters)Jim Langridge (Waters)Benito Cañas (Madrid)Lola Gutierrez (Madrid)Alberto Medina (Madrid)Trish Wheztel (U Penn)Eva Duchoslav (MDS Sciex)Jayson Falkner (U Michigan)David Horn (Agilent)

Henning Hermjakob (EBI)Andy Jones (U Liverpool)Sandra Orchard (EBI)Andreas Römpp (U Giessen)Marc Sturm (U Tübingen)Parag Mallick (Stanford)Norman Paton (Manchester)Ron Beavis (UBC)Ruedi Aebersold (ETHZ)Wilfred Tang (ABI)Rune PhilosofDavid Sparkman (U Pacific)Marius Kallhardt (Bruker)Nail Swainston (Manchester)Ruth McNally (Cardiff)Chris AllenPaul Rudnik (NIST)Steve Stein (NIST)Mi-Youn Brusniak (ISB)Dave Campbell (ISB)

Role Name

Chair Eric Deutsch, Institute for Systems Biology

Co-chairs Henning Hermjakob, European Bioinformatics InstituteAndy Jones, University of Liverpool

Secretary Sandra Orchard, European Bioinformatics Institute

MIAPE Pierre-Alain Binz, Swiss Institute for Bioinformatics

Ontology Gerhard Mayer, Medizinische Proteom-Center Bochum

Editors Martin Eisenacher, Medizinische Proteom-Center BochumAndy Jones, University of LiverpoolSylvie Ricard-Blum, University of Lyon

WG chairs Sandra Orchard (Molecular Interactions)

Eric Deutsch (Mass Spectrometry)

Andy Jones (Proteomics Informatics)

David Tabb (Quality Control)



Next meeting in Beijing on April 2017!