PRIDE and ProteomeXchange: supporting the cultural change in proteomics public data deposition

PRIDE and ProteomeXchange:
supporting the cultural change in
proteomics public data deposition
Dr. Juan Antonio Vizcaíno
Proteomics Team Leader
EMBL-EBI
Hinxton, Cambridge, UK

Juan A. Vizcaíno
juan@ebi.ac.uk
De.NBI Summer School 2016
Dagstuhl, 27 September 2016
Data resources at EMBL-EBI
Genes, genomes & variation
ArrayExpress
Expression Atlas
MetaboLights
PRIDE
InterPro Pfam UniProt
ChEMBL ChEBI
Molecular structures
Protein Data Bank in Europe
Electron Microscopy Data Bank
European Nucleotide Archive
European Variation Archive
European Genome-phenome Archive
Gene, protein & metabolite expression
Protein sequences, families & motifs
Chemical biology
Reactions, interactions &
pathways
IntAct Reactome MetaboLights
Systems
BioModels Enzyme Portal BioSamples
Ensembl
Ensembl Genomes
GWAS Catalog
Metagenomics portal
Europe PubMed Central
Gene Ontology
Experimental Factor
Ontology
Literature & ontologies

Juan A. Vizcaíno
juan@ebi.ac.uk
• PRIDE and ProteomeXchange
• How to submit data to PRIDE: PRIDE tools
• How to access data in PRIDE Archive
• Some examples of public data reuse
Overview

Juan A. Vizcaíno
juan@ebi.ac.uk
What is a proteomics publication in 2016?
• Proteomics studies generate potentially large amounts of
data and results.
• Ideally, a proteomics publication needs to:
• Summarize the results of the study
• Provide supporting information for reliability of any
results reported
• Information in a publication:
• Manuscript
• Supplementary material
• Associated data submitted to a public repository

Juan A. Vizcaíno
juan@ebi.ac.uk
• PRIDE stores mass spectrometry (MS)-
based proteomics data:
• Peptide and protein expression data
(identification and quantification)
• Post-translational modifications
• Mass spectra (raw data and peak
lists)
• Technical and biological metadata
• Any other related information
• Full support for tandem MS approaches
PRIDE (PRoteomics IDEntifications) database
http://www.ebi.ac.uk/pride/archive
Martens et al., Proteomics, 2005
Vizcaíno et al., NAR, 2016

Juan A. Vizcaíno
juan@ebi.ac.uk
Journal Submission Recommendations
• Journal guidelines recommend submission to proteomics
repositories:
 Proteomics (dataset briefs)
 JPR (HPP papers)
 Molecular and Cellular Proteomics
 Journals from the Nature group
 Journals from the PLOS group
• Funding agencies are enforcing public deposition of data
to maximize the value of the funds provided.

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE: Source of MS proteomics data
• PRIDE Archive already provides or
will soon provide MS proteomics
data to other EMBL-EBI resources
such as UniProt, Ensembl and the
Expression Atlas.
http://www.ebi.ac.uk/pride

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeXchange: A Global, distributed proteomics
database
PASSEL
(SRM data)
PRIDE
(MS/MS data)
MassIVE
(MS/MS data)
Raw
ID/Q
Meta
Mandatory raw data deposition
since July 2015
• Goal: Development of a framework to allow standard data submission and
dissemination pipelines between the main existing proteomics repositories.
http://www.proteomexchange.org
Vizcaíno et al., Nat Biotechnol, 2014

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeXchange: A Global, distributed proteomics
database
PASSEL
(SRM data)
PRIDE
(MS/MS data)
MassIVE
(MS/MS data)
Raw
ID/Q
Meta
jPOST
(MS/MS data)
Mandatory raw data deposition
since July 2015
• Goal: Development of a framework to allow standard data submission and
dissemination pipelines between the main existing proteomics repositories.
http://www.proteomexchange.org
New in 2016
Vizcaíno et al., Nat Biotechnol, 2014

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
Metadata /
Manuscript
Raw Data
Results
Journals
Peptide Atlas
Receiving repositories
PRIDE
Researcher’s results
Raw data
Metadata
PASSEL
Research
groups
Reanalysis of datasets
MassIVE
jPOST
MS/MS
data
(as complete
submissions)
Any other
workflow
(mainly partial
submissions)
DATASETS
SRM
data
Reprocessed results
MassIVE
ProteomeXchange data workflow

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
Metadata /
Manuscript
Raw Data
Results
Journals
UniProt/
neXtProtPeptide Atlas
Other DBs
Receiving repositories
PRIDE
GPMDBResearcher’s results
Raw data
Metadata
PASSEL
proteomicsDB
Research
groups
Reanalysis of datasets
MassIVE
jPOST
MS/MS
data
(as complete
submissions)
Any other
workflow
(mainly partial
submissions)
DATASETS
OmicsDI
Integration with other
omics datasets
SRM
data
Reprocessed results
MassIVE
ProteomeXchange data workflow

Juan A. Vizcaíno
juan@ebi.ac.uk
Countries with at least 100
datasets:
1105 USA
546 Germany
411 United Kingdom
356 China
229 France
188 Netherlands
178 Canada
150 Switzerland
125 Australia
123 Spain
123 Denmark
117 Japan
101 Sweden
ProteomeXchange: 4,534 datasets up until 31st July, 2016
Type:
4067 PRIDE (~90%)
339 MassIVE
115 PeptideAtlas/PASSEL
13 jPOST
Publicly Accessible:
2597 datasets, 57% of all
2334 PRIDE
135 MassIVE
115 PASSEL
13 jPOST
Datasets/year:
2012: 102
2013: 527
2014: 963
2015: 1758
2016 (till end of July): 1184
Top Species studied by at least 100
datasets:
2010 Homo sapiens
604 Mus musculus
191 Saccharomyces cerevisiae
140 Arabidopsis thaliana
127 Rattus norvegicus
936 reported taxa in total

Juan A. Vizcaíno
juan@ebi.ac.uk
• PRIDE Archive (in the context of ProteomeXchange
and the PSI standards)
• Some examples of public data reuse
Overview

Juan A. Vizcaíno
juan@ebi.ac.uk
Complete
Partial
Complete vs Partial submissions: processed results
For complete submissions, it is possible to connect the spectra with the identification
processed results (results can be parsed) and they can be visualized.

Juan A. Vizcaíno
juan@ebi.ac.uk
Complete vs Partial submissions: experimental metadata
Complete Partial
General experimental metadata about the projects is similar.
However, at the assay level information in partial submissions is not so detailed

Juan A. Vizcaíno
juan@ebi.ac.uk
Partial submissions can be used to store
other data types
• Everything can be stored, not only MS/MS data: very flexible
mechanism to be able to capture all types of datasets
• PRIDE does not store SRM data (it goes to PASSEL)
• Top down proteomics datasets.
• Mass Spectrometry Imaging datasets.
• Data independent acquisition techniques: e.g. SWATH-MS datasets.

Juan A. Vizcaíno
juan@ebi.ac.uk
How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to mzIdentML (or PRIDE XML)
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
submission tool)
• Post-submission steps

Juan A. Vizcaíno
juan@ebi.ac.uk
PX Data workflow for MS/MS data
1. Mass spectrometer output files: raw data (binary files) or
peak list spectra in a standardized format (mzML, mzXML).
2. Result files:
a. Complete submissions: Result files can be converted to
the mzIdentML data standard (also PRIDE XML).
b. Partial submissions: For workflows not yet supported by
PRIDE, search engine output files will be stored and
provided in their original form.
3. Metadata: Sufficiently detailed description of sample origin,
workflow, instrumentation, submitter.
4. Other files: Optional files:
a. QUANT: Quantification related results e. FASTA
b. PEAK: Peak list files f. SP_LIBRARY
c. GEL: Gel images
d. OTHER: Any other file type
Published
Raw
Files
Other
files

Juan A. Vizcaíno
juan@ebi.ac.uk
PX Data workflow for MS/MS data
1. Mass spectrometer output files: raw data (binary files) or
peak list spectra in a standardized format (mzML, mzXML).
2. Result files:
a. Complete submissions: Result files can be converted to
the mzIdentML data standard (also PRIDE XML).
b. Partial submissions: For workflows not yet supported by
PRIDE, search engine output files will be stored and
provided in their original form.
3. Metadata: Sufficiently detailed description of sample origin,
workflow, instrumentation, submitter.
4. Other files: Optional files (the list can be extended):
a. QUANT: Quantification related results e. FASTA
b. PEAK: Peak list files f. SP_LIBRARY
c. GEL: Gel images
d. OTHER: Any other file type
Published
Raw
Files
Other
files

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Components: Submission Process
PRIDE Converter 2
PRIDE Inspector PX Submission Tool
mzIdentML
PRIDE XML
1

Juan A. Vizcaíno
juan@ebi.ac.uk
Tools ‘RESULT’ file generation Final ‘RESULT’ file
mzIdentML
‘RESULT’
Now: native file export to mzIdentML
Spectra
files
(mzML,
mzXML,
mzData,
mgf,
pkl,
ms2,
dta, apl)
Mascot
ProteinPilot
Scaffold
PEAKS
MSGF+
PLGS
Native File export
Others

Juan A. Vizcaíno
juan@ebi.ac.uk
Complete submissions
Search
Engine
Results +
MS files
Search
engines
mzIdentML
- Mascot
- MSGF+
- MyriMatch and related tools from D. Tabb’s lab
- OpenMS
- PEAKS
- PeptideShaker
- ProCon (ProteomeDiscoverer, Sequest)
- Scaffold
- TPP via the idConvert tool (ProteoWizard)
- ProteinPilot (from version 5.0)
- X!Tandem native conversion (Beta, PILEDRIVER)
- Others: library for X!Tandem conversion, lab internal
pipelines, …
- Crux
An increasing number of tools support export to mzIdentML 1.1
- Referenced spectral files need to be submitted as well
(all open formats are supported).
Updated list: http://www.psidev.info/tools-implementing-
mzIdentML#.

Juan A. Vizcaíno
juan@ebi.ac.uk
Complete submissions: which tools are missing
Search
Engine
Results +
MS files
Search
engines
mzIdentML
- MaxQuant: Export to mzTab (work in progress)
-Proteome Discoverer (Thermo): Work in progress
An increasing number of tools support export to mzIdentML 1.1
Updated list: http://www.psidev.info/tools-implementing-
mzIdentML#.

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Converter 2
mzIdentML
PRIDE XML
2

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Inspector Toolsuite
Wang et al., Nat. Biotechnology, 2012
Perez-Riverol et al., Bioinformatics,
2015
Perez-Riverol et al., MCP, 2016
• PRIDE Inspector - standalone tool to enable visualisation and validation of MS
data.
• Build on top of ms-data-core-api - open source algorithms and libraries for
computational proteomics.
• Supported file formats: mzIdentML, mzML, mzTab (PSI standards), and PRIDE
XML.
• Broad functionality.
https://github.com/PRIDE-Utilities/ms-data-core-api
https://github.com/PRIDE-Toolsuite/pride-inspector

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Inspector Functionality
Summary and QC charts Peptide spectra annotation and
visualisation
Protein groups inference
 Protein view containing protein
inference information
 Quantification view
 Multiple export options (.mgf,
protein/peptide tables, mzTab file)
 Direct access to PRIDE datasets
 Summary and QC charts (Delta m/z,
precursor charges, etc.)
 Spectra view (fragmentation table, ion
series annotation)
 Protein inference algorithm and protein
groups visualisation

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Converter 2
mzIdentML
PRIDE XML
3

Juan A. Vizcaíno
juan@ebi.ac.uk
• Capture the mappings between the different types of files.
• Make the file upload process straightforward to the submitter (It transfers all the
files using Aspera or FTP).
PX submission tool
Published
Raw
Other
files
http://www.proteomexchange.org/submission
PX
submission
tool
• Command line alternative: Using the Aspera file transfer protocol.

Juan A. Vizcaíno
juan@ebi.ac.uk
PX submission tool: screenshots

Juan A. Vizcaíno
juan@ebi.ac.uk
Fast file transfer with Aspera
- Aspera is the default file transfer protocol to PRIDE:
- PX Submission tool
- Command line
- Up to 50X faster than FTP
File transfer speed should
not be a problem!!

Juan A. Vizcaíno
juan@ebi.ac.uk
Manuscript published detailing the process
Ternent et al., Proteomics, 2014http://www.proteomexchange.org/submission
Example dataset:
PXD000764
- Title: “Discovery of new CSF biomarkers for meningitis in children”
- 12 runs: 4 controls and 8 infected samples
- Identification and quantification data

Juan A. Vizcaíno
juan@ebi.ac.uk
Public data release: when does it happen?
• When the author tells us to do it (the authors can do it by
themselves)
• When we find out that a dataset has been published
• We look for PXD identifiers in PubMed abstracts.
• If your PXD identifier is not in the abstract, a paper may have
been published and the data is still private. Let us know!
• New web form in the PRIDE web to facilitate the process

Juan A. Vizcaíno
juan@ebi.ac.uk
• PRIDE Archive (in the context of ProteomeXchange
and the PSI standards)
• PRIDE Cluster and PRIDE Proteomes
Overview

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral: Centralised portal for all PX
datasets
http://proteomecentral.proteomexchange.org/cgi/GetDataset

Juan A. Vizcaíno
juan@ebi.ac.uk
RSS and Twitter feeds for public datasets
http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml
@proteomexchange

Juan A. Vizcaíno
juan@ebi.ac.uk
Ways to access data in PRIDE Archive
• PRIDE web interface
• File repository
• REST web service
• PRIDE Inspector tool

Juan A. Vizcaíno
juan@ebi.ac.uk
Vaudel M, Barsnes H, Berven FS, Sickmann A,
Martens L:
Proteomics 2011;11(5):996-9.
https://github.com/compomics/searchgui https://github.com/compomics/peptide-shaker
Vaudel M, Burkhart J, Zahedi RP, Berven FS, Sickmann A, Martens L,
Barsnes H:
Nature Biotechnology 2015; 33(1):22-24.
CompOmics Open Source Analysis Pipeline

Juan A. Vizcaíno
juan@ebi.ac.uk
Find the desired PRIDE project …
… and start re-analyzing the data!
… inspect the project details ….
Reshake PRIDE data!

Juan A. Vizcaíno
juan@ebi.ac.uk
Datasets are being reused more and more….
Data download volume for PRIDE in 2015: ~ 200 TB
Vaudel et al., Proteomics, 2016

Juan A. Vizcaíno
juan@ebi.ac.uk
Challenges for data reuse in proteomics
• Insufficient technical and biological metadata.
• Large computational infrastructure maybe needed (e.g. when
analysing many datasets together).
• Shortage of expertise (people).
• Lack of standardisation in the field.

Juan A. Vizcaíno
juan@ebi.ac.uk
Data sharing in Proteomics

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Cluster
• Provide an aggregated peptide centric view of PRIDE Archive
• Hypothesis: same peptide will generate similar MS/MS spectra across
experiments
• New spectral clustering algorithm to reliably group spectra coming from the
same peptide
• Infer reliable identifications by comparing submitted identifications of
spectra within a cluster
 After clustering, a representative spectrum is built for all peptides
consistently identified across different datasets Griss et al., Nat. Methods,
2013
Griss et al., Nat. Methods,
2016

Juan A. Vizcaíno
juan@ebi.ac.uk
Examples: one perfect cluster
- 880 PSMs give the same peptide ID
- 4 species
- 28 datasets
- Same instruments

Juan A. Vizcaíno
juan@ebi.ac.uk
Examples: one perfect cluster (2)

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Cluster as a Public Data Mining Resource
50
• http://www.ebi.ac.uk/pride/cluster
• Spectral libraries for 16 species.
• All clustering results, as well as specific subsets of interest available.
• Source code (open source) and Java API

Juan A. Vizcaíno
juan@ebi.ac.uk
Reprocess
• Data are reprocessed with the intention of obtaining
new knowledge or to provide an updated view on the
results.
• It mainly serves the same purpose of the original
experiment.
• For instance, a shot-gun dataset can be reprocessed
with a different algorithm or an updated sequence
database.

Juan A. Vizcaíno
juan@ebi.ac.uk
Reprocessing repositories
• These resources collect MS raw data and reprocess it using
one given analysis pipeline, and an up-to date protein
sequence database.
• Main resources: GPMDB and PeptideAtlas (ISB, Seattle).

Juan A. Vizcaíno
juan@ebi.ac.uk
PeptideAtlas builds
Examples of builds:
- Human
- Human plasma
- Human urine
- Drosophila
- Mouse
- Mouse plasma
- Cow
- Yeast
…

Juan A. Vizcaíno
juan@ebi.ac.uk
Draft Human proteome papers published in 2014
Wilhelm et al., Nature, 2014 Kim et al., Nature, 2014
•Two independent groups claimed to have produced the
first complete draft of the human proteome by MS.
• Some of their findings are controversial and need further
validation… but generated a lot of discussion and put
proteomics in the spotlight.
•They used many different tissues.
Nature cover 29 May 2014

Juan A. Vizcaíno
juan@ebi.ac.uk
Draft Human proteome papers published in 2014
Wilhelm et al., Nature, 2014
•Around 60% of the data used for the
analysis comes from previous
experiments, most of them stored in
proteomics repositories such as
PRIDE/ProteomeXchange, PASSEL or
MassIVE.
•They complement that data with “exotic”
tissues.

Juan A. Vizcaíno
juan@ebi.ac.uk
OmicsDI: Portal for omics datasets
http://www.ebi.ac.uk/Tools/omicsdi/
• Aims to integrate of ‘omics’ datasets (proteomics,
transcriptomics, metabolomics and genomics at present).
PRIDE
MassIVE
jPOST
PASSEL
GPMDB
ArrayExpress
Expression Atlas
MetaboLights
Metabolomics Workbench
GNPS
EGA
Perez-Riverol et al., 2016, BioRXxiv

Juan A. Vizcaíno
juan@ebi.ac.uk
OmicsDI: Portal for omics datasets
Perez-Riverol et al., 2016, BioRXxiv

Juan A. Vizcaíno
juan@ebi.ac.uk
• Main characteristics of PRIDE and ProteomeXchange
• PX/PRIDE submission workflow for MS/MS data
• PRIDE Inspector
• PX submission tool
• PRIDE/ProteomeXchange has become the de facto
standard for data submission and data availability in
proteomics
• Reuse/ reanalysis of proteomics data -> Many possible
applications
Conclusions

Juan A. Vizcaíno
juan@ebi.ac.uk
Aknowledgements: People
Attila Csordas
Tobias Ternent
Gerhard Mayer (de.NBI)
Johannes Griss
Yasset Perez-Riverol
Manuel Bernal-Llinares
Andrew Jarnuczak
Former team members,
especially Rui Wang, Florian
Reisinger, Noemi del Toro, Jose
A. Dianes & Henning Hermjakob
Acknowledgements: The PRIDE Team
All data submitters !!!

Juan A. Vizcaíno
juan@ebi.ac.uk
PSI Spring Meeting 2017
Beijing Proteome Research Center, China
April 24-26, 2017
April 23: 2nd PHOENIX Mini-Symposium
on Frontiers of Proteomics
April 27: Hiking the Great Wall
Focus topics:
• Quality control: qcML
• Proteogenomics formats
• proXI: proteomics eXpression Interface
• Privacy and Proteomics Data

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PRIDE and ProteomeXchange: supporting the cultural change in proteomics public data deposition