Proteomics services

Name Description ELIXIR Node

Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. 

The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:

 ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI

This project will be led by the ELIXIR Proteomics Community in collaboration with members of the Metabolomics Community and three ELIXIR platforms. High-throughput proteomics has become a popular choice in biological, biomedical and clinical studies and led to the development of hundreds of bioinformatics tools and data analysis pipelines. Given their large diversity, there is a urgent need to compare and benchmark different software pipelines over a large data spectrum.

This study aims to create the framework to benchmark proteomics data analysis workflows, to be built upon and improve resources from ELIXIR Tool, Data and Compute platforms by creating an interface between them linked with public proteomics data and open source stand-alone software and pipelines.

The involved data will be annotated with at least EOSC minimum information according to ELIXIR metadata standards. Our benchmarking will identify robust workflows and therefore nurture the proteomics community with high quality standards required for reproducible research and clinical applications.

 ELIXIR Denmark, EMBL-EBI, ELIXIR Netherlands, ELIXIR Spain, ELIXIR France, ELIXIR Sweden, ELIXIR Italy, ELIXIR Czech Republic, ELIXIR Germany

To dramatically improve the reusability of public proteomics datasets by substantially increasing the amount and quality of technical and biological annotations for datasets stored in the PRIDE database.

First, we will develop a posteriori annotation system for PRIDE, for both technical as well as biological metadata, which will leverage the unique synergies of already existing tools and pipelines developed by different ELIXIR nodes. Second, we will create data structures that can capture the most-frequently used experimental designs in proteomics studies. Third, an appropriate API will be built to allow annotation tools to be developed easily. Fourth, we will reach out to actively involve the whole proteomics community in the annotation process.

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

 EMBL-EBI, ELIXIR Belgium, ELIXIR Germany, ELIXIR Netherlands, ELIXIR Denmark, ELIXIR Switzerland, ELIXIR France, ELIXIR Sweden, ELIXIR Spain, ELIXIR Norway
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
EMBL-EBI

An ELIXIR implementation study started in February 2017, as a collaboration between EMBL-EBI and ELIXIR-DE. Its main objective is to develop open, robust, scalable and reproducible proteomics data analysis workflows based on OpenMS, directly connected to the PRIDE database (an ELIXIR core data resource) and to deploy these pipelines in the EMBL-EBI "Embassy Cloud" as a proof of concept.

Building on this work, we here propose a follow-up project that has three objectives: 

  1. The inclusion of additional open tools developed by other ELIXIR nodes
  2. The improvement of the overall infrastructure supporting the implementation of proteomics data analysis pipelines
  3. The inclusion of quality control pipelines.

The overarching goal is that these tools can be deployed in other cloud infrastructures, and can be easily reused by anyone in the community, thus bringing the users closer to the tools, and the tools closer to the data.

Impact of the study

The outcome will be that an increased range of open proteomics tools will be included in an extended range of cloud infrastructures, including new quality control features based on OpenMS. Impact – increased facility for proteomics analysis across multiple cloud platforms – all with increased degree of quality control.

 ELIXIR Belgium, EMBL-EBI, ELIXIR Germany, ELIXIR France, ELIXIR Spain

Theme: Linking Data

Today, research generates more data than ever, and a multitude of experimental data types. Such data types are often connected at source: perhaps generated from the same samples or as part of the same study. It is important that different data types are made available for re-use in a linked and coordinated manner, enabling full reuse of all the data in integrated analysis. Experimental data types are often siloed in varied specialised repositories, using different metadata models, so linking them is not straightforward. Also, data obtained from living humans is sensitive and shared under a controlled access model, adding an extra layer of complexity.

In this project, partners will establish a strong foundation for developing solutions to integrate multi-omic sensitive data effectively among FEGA nodes, biobanks and ELIXIR Core Data Resources such as PRIDE and GWAS Catalog. Five ELIXIR Nodes will be involved, as well as the Polish FEGA node (in-kind contribution) from two ELIXIR Communities (Federated Human Data and Proteomics), spanning three diverse data use cases to address the challenges of this open call.

The project will start by developing a comprehensive landscape analysis of current human data linkage challenges and solutions (Task 1). Based on this, concrete models and prototypes will be proposed to link sensitive proteomics data (Task 2), cohorts and biobank data (Task 3), and population cohort-derived data (Task 4) to genomics data. Results from tasks 2 to 4 will be used to improve the FEGA metadata model. The project will result in more coherent data deposition, discoverability and retrieval of multi-omics datasets, providing FAIRer data, and accelerating research. To facilitate broad engagement, the project will engage the ELIXIR Communities through dedicated online and in-person events, where both interim and final results of the project will be disseminated.

 ELIXIR Finland, ELIXIR Germany, ELIXIR Spain, ELIXIR Sweden, EMBL-EBI
ELIXIR France

Human data and translational research is a high priority for ELIXIR and builds on the progress made in the previous programmes by the Human Data Communities. Within the Science tier of the ELIXIR 2024–2028 Programme, advances will be focussed on enabling researchers (including research clinicians) to use ELIXIR’s infrastructure, for human genomic, phenotypic, imaging and demographic data to support discovery, analysis, innovation and integration of research findings into the clinic and healthcare. More specifically, through these projects we will ensure that millions of human genomes are discoverable and exploited in a biomedical setting through ELIXIR-supported infrastructure and community-endorsed standards, software, workflows and analysis environments across ELIXIR Nodes. 

On Data Deposition:

On Federated Data Analysis:

On Linking Data:

 ELIXIR Belgium, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

Resulting from the work performed in previous and/or ongoing ELIXIR implementation studies (IS) led by the ELIXIR Proteomics Community, PRIDE public proteomics datasets including metadata annotations using the Sample and Data Relationship Format (SDRF) as well as some open proteomics data analysis pipelines are starting to be available.

In this proposed follow-on IS previous results/outputs will be used as the base to develop a set of open and user-friendly analysis pipelines, which will be applied to assess the possibilities for performing more automated re-analyses using the metadata SDRF-encoded annotations of public datasets, not only at an identification but also on a quantitative and a statistical level for both data-dependent acquisition (DDA) and data-independent acquisition (DIA) datasets. Additionally, common ideas in this context and in others overlapping topics of interest will be explored e.g. in a joint gap analysis performed between the ELIXIR Proteomics with the IDP and 3D-BioInfo ELIXIR Communities, to further serve the overall ELIXIR goals.

This study provides a well-documented use case, which will motivate users to perform SDRF-annotations of public datasets. By developing and providing the community with data processing and analysis pipelines as well as by helping to standardize data management and annotation, two goals of the proteomics community will be addressed.

 ELIXIR Germany, ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Denmark, EMBL-EBI, ELIXIR Finland, ELIXIR France, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Sweden

The ELIXIR Metabolomics Community relies on standards, formats and data treatment solutions development and adoption, but it remains challenging to ensure high-quality reported metadata, sufficiently contextualised results, interoperable and reusable datasets and to integrate these metabolomics data with other omics or studies. 

This project is designed to address these issues and aims to connect key international standards with ELIXIR resources, as well as creating associated community guidelines and training materials. 

Based on the FAIRification framework, activities in the project will:

  • Increase interoperability and reuse of public metabolomics datasets and workflows through enhanced and extended open data standards, resources and new semantic annotations
  • Define, ensure and establish quality control for study baselines in Metabolomics and Exposomics
  • Facilitate metabolomic data interpretation and meta-analysis integration with multi-omics and systems biology studies

As a first necessary step, the project will create a Semantic Metabolomics Data Model to standardise metadata, ensuring unambiguous reuse of metabolomics projects. This model will focus on integrating key ontologies, providing open training initiative and enhancing the interoperability of metabolomics data through the production of open guidelines for annotation steps. By linking with ELIXIR’s Deposition databases, ISA Framework and other services, the project seeks to boost interconnection with ELIXIR platforms, other ELIXIR communities (Systems Biology, Food and Nutrition, Galaxy, Proteomics, Toxicology, Research Data Alliance Focus Group, etc.), the FAIR Cookbook and BioSchemas.org communities. Project outcomes are expected to promote  the emergence of ambitious and innovative semantic-based solutions for inter-comparison of studies in healthcare, clinical and plant domains.

 ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Italy, ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR UK, EMBL-EBI
ELIXIR Finland, ELIXIR Germany, ELIXIR Spain, ELIXIR Sweden, EMBL-EBI