PRIDE and ProteomeXchange

PRIDE resources and ProteomeXchange
Dr. Juan Antonio Vizcaíno
EMBL-EBI
Hinxton, Cambridge, UK

Juan A. Vizcaíno
juan@ebi.ac.uk
WT Proteomics Bioinformatics Course 2016
Hinxton, 20 July 2017
Data resources at EMBL-EBI
Genes, genomes & variation
ArrayExpress
Expression Atlas 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 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 Archive (in the context of ProteomeXchange
and the PSI standards)
• How to submit data to PRIDE: PRIDE tools
• How to access data in PRIDE Archive
• PRIDE Cluster
Overview

Juan A. Vizcaíno
juan@ebi.ac.uk
• PRIDE Archive (in the context of
ProteomeXchange and the PSI standards)
• How to submit data to PRIDE: PRIDE tools
• How to access data in PRIDE Archive
• PRIDE Cluster
Overview

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
• Any type of data can be stored.
PRIDE (PRoteomics IDEntifications) Archive
http://www.ebi.ac.uk/pride/archive
Martens et al., Proteomics, 2005
Vizcaíno et al., NAR, 2016

Juan A. Vizcaíno
juan@ebi.ac.uk
Stats: Data submissions to PRIDE Archive continue to increase
1,950 datasets submitted to PRIDE Archive in 2016

Juan A. Vizcaíno
juan@ebi.ac.uk
Data content in PRIDE Archive
• Submission driven resource
• PRIDE is split in datasets (group of assays)
• An assay represents one MS run (in most cases).
• PRIDE aims to represent the author’s view on the data
• No data reprocessing at present (but this will soo change).
• Supported formats for the results: mzIdentML and mzTab
(and PRIDE XML).

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
Deutsch et al., NAR, 2017

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
Vizcaíno et al., Nat Biotechnol, 2014
Deutsch et al., NAR, 2017

Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
Metadata /
Manuscript
Raw Data
Results
Journals
UniProt/
neXtProtPeptide Atlas
Other DBs
PRIDE
GPMDBResearcher’s results
Raw data
Metadata
PASSEL
proteomicsDB
Research
groups
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

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

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 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
How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission
• File conversion/export to mzIdentML (soon to mzTab,
PRIDE XML is no longer recommended)
• 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 (or mzTab) data standard (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 (or mzTab) data standard (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: Data Submission Process
PRIDE Inspector PX Submission Tool
PRIDE Converter 2
PRIDE XML
Not recommended
mechanism
In addition to PRIDE Archive, the PRIDE team develops
and maintains different tools and software libraries to
facilitate the handling and visualisation of MS proteomics
data and the submission process
mzIdentML
(mzTab)

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

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
- Soon: ProteomeDiscoverer (Thermo), PLGS
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
Tools ‘RESULT’ file generation Final ‘RESULT’ file
mzTab
‘RESULT’
Coming soon: Support for mzTab
Spectra
files
(mzML,
mzXML,
mzData,
mgf,
pkl,
ms2,
dta, apl)
Mascot
MaxQuant
Others
Native File export

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Components: Submission Process
2
mzIdentML
(mzTab)

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Inspector Toolsuite
Wang et al., Nat. Biotechnology, 2012
Perez-Riverol et al., MCP, 2016
PRIDE Inspector
PRIDE Inspector 2 supports:
- PRIDE XML
- mzIdentML + all types of spectra files
- mzML
- mzTab identification and Quantification (+
all types of spectra files)
https://github.com/PRIDE-Toolsuite/

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Inspector Toolsuite
PRIDE Inspector 2
https://github.com/PRIDE-Toolsuite/
New visualisation
functionality for Protein
Groups

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Components: Submission Process
3
mzIdentML
(mzTab)

Juan A. Vizcaíno
juan@ebi.ac.uk
PX Submission Tool
 Desktop application for data
submissions to ProteomeXchange via
PRIDE
• Implemented in Java 7
• Streamlines the submission process
• Capture mappings between files
• Retain metadata
• Fast file transfer with Aspera (FASP®
transfer technology) – FTP also
available
• Command line option
Submission tool screenshot

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

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE/PX EXERCISE

Juan A. Vizcaíno
juan@ebi.ac.uk
Workflow Raw data
mgf
PS
output
mzIdentML
PeptideShaker
PRIDE Inspector
PX/ PRIDE
Your own workflow:
MS/MS
data processing
peak list generation
PX submission tool
PeptideShaker

Juan A. Vizcaíno
juan@ebi.ac.uk
In the first part of the exercise…
• You will use PeptideShaker to export the results of an
analysis to mzIdentML v1.1 (format required for the
submission)
• You will learn how to use PRIDE Inspector (tool for the
visualization and analysis of proteomics data)
• You will learn how to use the PX submission tool, to
perform data submissions to PRIDE/PX

Juan A. Vizcaíno
juan@ebi.ac.uk
Time to Work on it…

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
Partial submissions can be used to store other data
types
93.6% of the datasets
come from DDA/ shot-gun
approaches

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
PRIDE Archive web interface

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Archive web interface (2)

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
Public datasets from different omics: OmicsDI
http://www.omicsdi.org/
• 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., Nat Biotechnol, 2017

Juan A. Vizcaíno
juan@ebi.ac.uk
OmicsDI: Portal for omics datasets

Juan A. Vizcaíno
juan@ebi.ac.uk
Second part of the exercise…
• Choice of 2 exercises:
1. PRIDE Archive web interface (search/ browse PRIDE
data in the web - beginner)
2. PRIDE Archive API web service (search/ browse PRIDE
data programmatically - intermediate)

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Archive web interface: Get familiarized with it

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Archive API
for project in projects:
# Set the request URL
url = 'http://www.ebi.ac.uk:80/pride/ws/archive/file/list/project/' + project
# Create the request
req = urllib.request.Request(url)

Juan A. Vizcaíno
juan@ebi.ac.uk
• You have learnt how to use:
• PeptideShaker export to mzIdentML
• PRIDE Inspector
• PX submission tool
• PX/PRIDE complete submission requirements.
• How to use the PRIDE Archive web interface
• How to use PRIDE API
Conclusions of the exercise

Juan A. Vizcaíno
juan@ebi.ac.uk
Added value resources: PRIDE Cluster
• Condensed and across-data set, QC-filtered view on
PRIDE data.
• PRIDE Cluster: Peptide centric.

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 version of spectral clustering algorithm to reliably group spectra
coming from the same peptide.
• Enables QC of peptide-spectrum matches (PSMs). 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.
 Used to build spectral libraries (for 16 species).
Griss et al., Nat. Methods, 2013
Griss et al., Nat. Methods, 2016

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

Juan A. Vizcaíno
juan@ebi.ac.uk
PRIDE Cluster as a Public Data Mining Resource
51
• 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
PRIDE data
dissemination

Juan A. Vizcaíno
juan@ebi.ac.uk
• Main characteristics of PRIDE Archive 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
• PRIDE Cluster: added-value resource
Conclusions

Juan A. Vizcaíno
juan@ebi.ac.uk
Do you want to know a bit more…?
http://www.slideshare.net/JuanAntonioVizcaino

Juan A. Vizcaíno
juan@ebi.ac.uk
Aknowledgements: People
Attila Csordas
Tobias Ternent
Mathias Walzer
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 !!!
@pride_ebi
@proteomexchange

Juan A. Vizcaíno
juan@ebi.ac.uk

PRIDE and ProteomeXchange

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