Introduction to PRIDE Database for Human Microbiome

Introduction to the PRIDE database for the
Human Microbiome Project
Dr. Juan Antonio Vizcaíno
PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hinxton, Cambridge, UK

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
• What is PRIDE?
• The ProteomeXchange Consortium
• Submission process and PRIDE tools
• Miscellaneous
Overview

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Data resources at EMBL-EBI
Genes, genomes & variation
RNA Central
ArrayE
xpress
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
11 December 2015
PRIDE (PRoteomics IDEntifications) Archive
http://www.ebi.ac.uk/pride
• PRIDE Archive 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
Martens et al., Proteomics, 2005
Vizcaíno et al., NAR, 2016, in press

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Data content in PRIDE Archive
• PRIDE is organised in datasets (or group of assays).
• An assay represents one MS run (in most cases).
• Focused in MS/MS approaches, but any type of proteomics
workflows can be stored.
• For each dataset PRIDE stores at least the raw data and the
processed results.

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
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
11 December 2015
PRIDE Archive submitted datasets up until 1st November, 2015
• 1,259 submitted datasets to PRIDE Archive by November 1st
• 923 were submitted datasets in 2014
• In the last 6 months, 155 submitted datasets per month
• Size: ~ 160 TB

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Access statistics: PRIDE Archive via the file repository
Data download figures:
153.5 TB downloaded so far in 2015 by FTP
22.6 TB so far in 2015 by Aspera
So far, 176 TB in 2015 (by mid November)
156 TB in 2014
FTP access for 2015, split per month

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
ProteomeXchange Consortium
• Goal: Development of a framework to allow standard
data submission and dissemination pipelines
between the main existing proteomics repositories.
• Includes PeptideAtlas (ISB, Seattle), PRIDE
(Cambridge, UK) and (very recently) MassIVE (UCSD,
San Diego).
• Common identifier space (PXD identifiers)
• Two supported data workflows: MS/MS and SRM.
• Main objective: Make life easier for researchers
http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
ProteomeCentral
Metadata /
Manuscript
Raw Data*
Results
Journals
UniProt/
neXtProt
Peptide Atlas
Other DBs
Receiving repositories
PASSEL
(SRM data)
PRIDE
(MS/MS data)
Other DBs
GPMDB
Researcher’s results
Reprocessed results
Raw data*
Metadata
MassIVE
(MS/MS data)
Vizcaíno et al., Nat Biotechnol, 2014
ProteomeXchange data workflow

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
ProteomeCentral: Portal for all PX datasets
http://proteomecentral.proteomexchange.org/cgi/GetDataset

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
ProteomeXchange: 2,774 datasets up until 1st September, 2015
Type:
1681 PRIDE partial
813 PRIDE complete
173 MassIVE
84 PeptideAtlas/PASSEL complete
23 Reprocessed
Publicly Accessible:
1372 datasets, 49% of all
90% PRIDE
6% PASSEL
4% MassIVE
Data volume:
Total: ~150 TB
Number of all files: ~400,000
PXD000320-324: ~ 4 TB
PXD002319-26 ~2.4 TB
PXD001471 ~1.6 TB
Datasets/year:
2012: 102
2013: 527
2014: 963
2015: 1182
Top Species studied by at least 20 datasets:
1080 Homo sapiens
335 Mus musculus
110 Saccharomyces cerevisiae
98 Arabidopsis thaliana
75 Rattus norvegicus
58 Escherichia coli
29 Bos taurus
23 Glycine max
20 Caenorhabditis elegans
20 Oryza sativa
~ 500 species in total
Origin:
714 USA
313 Germany
252 United Kingdom
163 China
146 France
121 Netherlands
108 Switzerland
103 Canada
81 Denmark
73 Spain
68 Japan
67 Australia
63 Sweden
57 Belgium
43 Austria
39 India
34 Taiwan
33 Norway
26 Italy
24 Ireland
24 Finland
21 Republic of Korea
20 Brazil
20 Russia
18 Israel
18 Singapore …

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
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
PRIDE XML or the mzIdentML data standard.
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
11 December 2015
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.
Processed results are available in an open data standard:
mzIdentML or in the older PRIDE XML format

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
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
11 December 2015
Public metaproteomics data in PRIDE Archive so far…
28 public datasets:
- 10 Complete
- 15 Partial
(3 before PX)

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PRIDE Tools: Submission Process
PRIDE Converter 2
PRIDE Inspector PX Submission Tool
mzIdentML
PRIDE XML
1

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Tools ‘RESULT’ file generation Final ‘RESULT’ file
mzIdentML
‘RESULT’
Now: native file export
Spectra
files
Mascot
ProteinPilot
Scaffold
PEAKS
MSGF+
Others
Native File export

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
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
11 December 2015
Search
output
files
Spectra
files
Original data files ‘RESULT’ file generation Final ‘RESULT’ file
PRIDE
XML
‘RESULT’
Before: only file conversion to PRIDE XML
File conversion
PRIDE
Converter

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PX Data workflow for MS/MS data
Search
Engine
Results + MS
files
PRIDE
Converter 2
PRIDE XML
Coté & Griss et al., MCP, 2012
Other tools available:
- PRIDE Converter
- PLGS (Waters)
- Proteios
- EasyProt
- hEIDI
- OmicsHub (Integromics)
- PeptideShaker (Compomics)
PRIDE Converter 2
https://github.com/PRIDE-Toolsuite/pride-converter-2
- ‘Bulk’ conversion possible: Command Line mode
- Virtually no limit in file sizes.

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PRIDE Converter 2
mzIdentML
PRIDE XML
2

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PRIDE Inspector Toolsuite: Visualisation tool
Wang et al., Nat. Biotechnology, 2012
Perez-Riverol et al., MCP, 2016, in press
PRIDE Inspector Toolsuite
PRIDE Inspector Toolsuite 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
11 December 2015
Example visualisation: PXD000164
Lassek et al., MCP, 2015

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PRIDE Inspector Toolsuite: Visualisation tool

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PRIDE Converter 2
mzIdentML
PRIDE XML
3

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
• It selects and captures the mappings between the different types of files included in the
submission.
• It transfers all the files using Aspera (default) or FTP.
PX submission tool
Results
Raw
Other
files
http://www.proteomexchange.org/submission
PX
submission
tool
• Version 2.3.0 released in August 2015 (Several refinements and improvements).
• Alternative command line method also available for groups with bioinformatics support.

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
PX submission tool: screenshots

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
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
11 December 2015
Manuscript published detailing the process
Ternent et al., Proteomics, 2014http://www.proteomexchange.org/submission-proteomexchange-pride
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
11 December 2015
Partial submissions can be used to store other data
workflows
• Everything can be stored, not only MS/MS data (~90% of datasets):
very flexible mechanism to be able to capture all types of datasets
• PRIDE Archive does not store SRM data (it goes to PASSEL, PX
partner).
• Top down proteomics datasets (19 public datasets).
• Mass Spectrometry Imaging datasets (1 public dataset).
• Data independent acquisition techniques: e.g. SWATH-MS (22 public
datasets), MSE (5 public datasets) HDMSE (2 public datasets).

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Linking of datasets from other omics fields
• Samples IDs can be included during the submission process (e.g.
in the PX submission tool), but they are not linked at present .
• Ongoing general EBI approach to improve the current situation,
working closely with the EBI BioSamples database.
• Better integration of IDs from the NCBI Biosamples DB should also
be possible.
• So far, we have not had an “example” project and dedicated funding
to do this.

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Sneak peak to other PRIDE resources
• Provide an aggregated and QC filtered peptide-centric
and protein centric view on PRIDE Archive data.
http://www.ebi.ac.uk/pride/cluster/http://wwwdev.ebi.ac.uk/pride/proteomes/
Griss et al., Nat Methods, 2013

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Do you want to know a bit more…?
http://www.slideshare.net/JuanAntonioVizcaino

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Aknowledgements: People
Attila Csordas
Tobias Ternent
Noemi del Toro
Gerhard Mayer (Bochum, de.NBI)
Johannes Griss
Yasset Perez-Riverol
Henning Hermjakob
Former team members: Rui Wang,
Florian Reisinger and Jose A. Dianes
The PRIDE Team

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Discussion

Juan A. Vizcaíno
juan@ebi.ac.uk
11 December 2015
Questions?

Introduction to PRIDE Database for Human Microbiome

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