Proteomics Community

Proteomics is the large-scale experimental study of the proteome, which is all the proteins that are produced or modified by an organism or system. Proteomics can tell us about when and where proteins are expressed, the rates of protein production and degradation, characterisation of protein post-translational modifications (e.g. phosphorylation), elucidating protein structures, and protein-protein interactions.

This information can be combined with data from other omics disciplines (genomics, metagenomics, metabolomics) to give us greater insights into how organisms work.

The goal of the ELIXIR Proteomics Community is to develop and maintain sustainable proteomics tools and data resources. An essential part of the development will also be the ‘FAIRification’ of the resources (i.e. making the resources FAIR - Findable, Accessible, Interoperable, and Reusable).

Goals of the Community

The ELIXIR Proteomics Community was created in September 2017 and its goals are:

To improve how proteoform data is collected and integrated with other omics data

  • Proteoforms are the different molecular forms that a protein produced by a single gene can take. Different proteoforms can have different biological functions or can be disease biomarkers.
  • Current proteomics data analysis does not provide sufficient depth and accuracy to distinguish between proteoforms, so the proteomics community aims to create resources for handling, analysing and validating proteoforms. This will include creating data standards for proteoform description and detection.
  • The Community will also make multi-omics data sets available – and findable – for a larger community. This will make it easier to integrate proteomics data with other omics data, and enable greater insights into the relationships between proteoforms, genes, metabolites and other meta-scale entities.
  • The Community is conducting an Implementation Study called Mining the proteome: Enabling automated processing and analysis of large-scale proteomics data, which runs until June 2018.

To develop data processing and analysis pipelines in proteomics

  • The Community aims to develop open, scalable, user-friendly and quality controlled data analysis pipelines. These could be used in different compatible software environments, including cloud infrastructures.
  • Users should have access to the tools of their choice for the main experimental approaches in the field, such as data-dependent acquisition (DDA), data-independent acquisition (DIA), and targeted approaches like Selected Reaction Monitoring.

To help standardise data management and annotation in proteomics

  • The Community aims to develop guidelines and tools for the improvement of proteomics data set annotation, as well as extend data repositories such as PRIDE (an ELIXIR core data resource) to facilitate public data reuse.
  • It also aims to develop and implement guidelines and software for managing identifiable human (clinical) data from proteomics analyses.

Commissioned Services

ELIXIR funds a number of short-term technical projects called Commissioned Services. The Proteomics Community is currently involved in the following:

For completed projects the Community has been involved in see the Commissioned services page.


Juan Vizcaino
Juan Antonio Vizcaíno
Oliver Kohlbacher
Oliver Kohlbacher
(ELIXIR Germany)
Lennart Martens
Lennart Martens
(ELIXIR Belgium)

Find out more

  • Vizcaíno JA, Walzer M, Jiménez RC et al. A community proposal to integrate proteomics activities in ELIXIR [version 1; referees: 2 approved]. F1000Research 2017, 6:875 (doi: 10.12688/f1000research.11751.1)
  • Contact proteomics-coleads [at] if you'd like to know more about the community's work.
  • Introduction to proteomics (EMBL-EBI Train online)