Proteomics data standards

Introduction to the PSI standard data formats
Dr. Juan Antonio Vizcaíno
EMBL-EBI
Hinxton, Cambridge, UK

Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2017
Hinxton, 19 July 2017
Overview
• A couple of slides about the need of data standards
• The Proteomics Standards Initiative
• Existing data standards

Juan A. Vizcaíno
juan@ebi.ac.uk
Standards are needed in real life: also in bioinformatics…
With a small number
of standards,
converters are feasible
Data standards are needed

Juan A. Vizcaíno
juan@ebi.ac.uk
Taken from Biocomicals, http://biocomicals.blogspot.com

Juan A. Vizcaíno
juan@ebi.ac.uk
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/MRM/PRM (Selected/ Multiple/Parallel Reaction
Monitoring)

Juan A. Vizcaíno
juan@ebi.ac.uk
•Develops data standards for proteomics.
•Both data representation and annotation standards.
•Involves data producers, database providers, software producers,
publishers, everyone who wants to be involved…
•Active Workgroups: MI, MS, PI, Mod and the new QC.
•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 (MSI).
http://www.psidev.info
HUPO Proteomics Standards Initiative

Juan A. Vizcaíno
juan@ebi.ac.uk
PSI Deliverables
•Minimum information (MIAPE) specifications: Format-independent
specification of minimum information guidelines.
•Formats: Usually XML-based (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 open 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
PSI MS Controlled Vocabulary
Mayer et al., Database, 2013~2,700 terms by June 2017

Juan A. Vizcaíno
juan@ebi.ac.uk
The Ontology Lookup Service (OLS)
http://www.ebi.ac.uk/ontology-lookup/

Juan A. Vizcaíno
juan@ebi.ac.uk
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
•MS data: mzML (also used in MS metabolomics).
•Protein and peptide identification: mzIdentML.
•Peptide and protein quantification: mzQuantML.
•SRM transitions (for targeted proteomics): TraML.
•Molecular interactions: PSI MI XML and MITAB.
• 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
Current PSI Standard File Formats for MS
• mzMLMS data
• mzIdentMLIdentification
• mzQuantMLQuantitation
• mzTabFinal Results
• TraMLSRM

Juan A. Vizcaíno
juan@ebi.ac.uk
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
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 the near
future.
Martens et al., MCP, 2011

Juan A. Vizcaíno
juan@ebi.ac.uk
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
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
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*.
• Version 1.2 just published (May 2017).
• 2012-2016:
• 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
mzIdentML 1.1
Data standard for peptide
and protein identification
data
mzIdentML 1.2
2011-
2012
2017
New support for:
- Cross-linking approaches
- Peptide level scores
- Modification localization scores
- Proteogenomics approaches
Improved support for:
- Protein inference
- Pre-fractionation
- de novo sequencing
- Spectral library searches
Increasingly
supported
by the most-
used
proteomics
software
and
databases
jmzIdentML
mzid Library
ms-data-core-api
MyriMatch
ProteoAnnotator
PIA
ProCon

Juan A. Vizcaíno
juan@ebi.ac.uk
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 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
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
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
Metadata section - Example

Juan A. Vizcaíno
juan@ebi.ac.uk
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
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
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
Vizcaíno et al., MCP, 2017
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

Juan A. Vizcaíno
juan@ebi.ac.uk
Importance of making software available
jmzML (https://github.com/PRIDE-Utilities/jmzml) Cote et al., Proteomics, 2009
jmzIdentML (https://github.com/PRIDE-Utilities/jmzidentML) Reisinger et al., Proteomics, 2012
jmzReader (https://github.com/PRIDE-Utilities/jmzReader) Griss et al., Proteomics, 2012
jmzQuantML (https://github.com/UKQIDA/jmzquantml) Qi et al., Proteomics, 2014
jmzTab (https://github.com/PRIDE-Utilities/jmzTab) Xu et al., Proteomics, 2014
ms-data-core-api (https://github.com/PRIDE-Utilities/ms-data-core-api)Perez-Riverol et al., Bioinformatics, 2015
PSI promotes implementations. The reference libraries are always
open source and can be used by anyone!

Juan A. Vizcaíno
juan@ebi.ac.uk
Proteogenomics related data formats
• Two ongoing formats are being developed: proBed
(version 1 available) and proBAM (still under review).
• Same overall objective: to map identified peptides to
genome coordinates.
• Different level of detail:
• proBed is tab-delimited and simpler, based on the original
BED format. Less level of detail.
• proBAM is based in the original SAM/BAM formats, widely
used in genomics. Much higher level of detail.

Juan A. Vizcaíno
juan@ebi.ac.uk
Provide your own data to genome browsers

Juan A. Vizcaíno
juan@ebi.ac.uk
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
Do you want to learn more?

Juan A. Vizcaíno
juan@ebi.ac.uk

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