PowerPoint Presentation

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