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Enabling automated processing and analysis of large-scale proteomics dataJuan Antonio Vizcano, EMBL-EBIHinxton, Cambridge
www.elixir-europe.orgELIXIR All Hands 2017, 21-23 March, Rome, Italy
One slide intro to MS based proteomics
Hein et al., Handbook of Systems Biology, 2012
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
Kickoff meeting for Proteomics activities in ELIXIR
It took place on March 1-2 2017, at Tuebingen, organised by ELIXIR-Germany.
~25 people attending, representing 11 ELIXIR Nodes.
Outcome: White paper outlining the possible future activities related to proteomics in the context of ELIXIR. This paper will be submitted to F1000 Research.
To be available by end of May/ beginning of June.
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
ELIXIR Implementation Project
1-year project just started. Led by EMBL-EBI (Vizcano) and ELIXIR-Germany (Kohlbacher, Eisenacher).
Aim: Development of reproducible data analysis pipelines for shot-gun proteomics approaches using the OpenMS framework.
Deployment of the pipelines in the EMBL-EBI Embassy cloud as proof of concept:Facilitate future deployment in other cloud environments.
Direct connection with public datasets in the PRIDE database.
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
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PRIDE is the word-leading mass spectrometry (MS)-based proteomics data repository.
It stores:Peptide and protein expression data (identification and quantification)Post-translational modificationsMass spectra (raw data and peak lists)Technical and biological metadataAny other related information
Any data workflow is now supported.Leading the global ProteomeXchange Consortium.
PRIDE (PRoteomics IDEntifications) Archivehttp://www.ebi.ac.uk/pride/archiveMartens et al., Proteomics, 2005Vizcano et al., NAR, 2016
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
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Why this project is timely? Martens & Vizcano, Trends Bioch Sci, 2017
Data download from PRIDE in 2016: 243 TB
Open, reproducible, traceable and scalable analysis pipelines are needed, as the size of proteomics datasets keeps growing.Reuse of public proteomics data is flourishing.
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
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Aknowledgements: PeopleMathias WalzerYasset Perez-Riverol
EMBL-EBI cloud team (led by Steven Newhouse)
Oliver Kohlbacher (Tuebingen University)
Martin Eisenacher (Bochum University)
Everyone who attended the workshop in Tuebingen (March 1-2)
Do you want to get involved?
Acknowledgements
ELIXIR All Hands 2017, 21-23 March, Rome, Italy
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www.hupo2017.ie
Abstract Deadline: 5th AprilEarly Registration Deadline: 14th June Dublin 17-21st September
ELIXIR All Hands 2017, 21-23 March, Rome, Italy