European Bioinformatics Community for Mass Spectrometry
The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) is an initiative for mass spectrometry (MS) related bioinformatics. Its aim is to improve bioinformatics for MS-based omics research through the setup of community-driven initiatives improving the collaboration, funding, publication, and training activities.
Mass spectrometry-based omics (such as proteomics) experiments, require expertise in a combination of scientific fields, including bioinformatics and biostatistics. While these fields are of critical importance, they are unfortunately not always the expertise of all scientists involved. Even worse, it is often difficult to find educational resources, help and support for computational proteomics. Consequently, users have false expectations about the bioinformatics tools available. To this end, we started the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) initiative in November 2015 to bring together the bioinformatics community. The intention of this community is to provide an open, collaborative and constructive environment. The initiative is carried enthusiastically by the bioinformatics community and welcomes everyone willing to help.
EuBIC-MS organizes a dedicated yearly conference in computational MS, bringing together top omics bioinformatics researchers, junior scientists and industry partners from across Europe. Every year, this conference alternates between a Winter School with keynote talks and workshops, and a Developers’ Meeting with hackathons. On top, the EuBIC-MS initiative provides various workshops all over the European MS and proteomics conferences, as well as contributing to conference bioinformatics hubs.
The EuBIC-MS Winter School on computational mass spectrometry (MS) takes place every two years. Its aim is to bring together the users and developers of computational mass spectrometry tools, as well as academia and industry. The winter school starts with an educational day dedicated to workshops and trainings in established computation MS tools and workflows. The following days, internationally renowned invited speakers give lectures and practical workshops covering the aspects of identification, quantification, result interpretation, and integration of MS data.
The next Winter School will take place 15-19 January 2024 in Winterberg, Germany. Save the date!
Past and upcoming Winter Schools:
The EuBIC-MS Developers Meeting is organized each second year. This meeting is aimed at bringing together computer scientists and developers in the field of mass spectrometry-related bioinformatics to discuss and work together in an open and constructive spirit. The program is split between keynote lectures and multiple hackathon sessions where the participants develop bioinformatics tools and resources addressing outstanding needs in the mass spectrometry-related bioinformatics and user community.
Past and upcoming Developers Meetings:
During the yearly in-person EuBIC-MS Organizational Meeting, a series of talks or workshops is often hosted as well. This is the perfect opportunity for EuBIC-MS members to present their work to the local proteomics and mass spectrometry communities in a friendly and open atmosphere.
Past and upcoming EuBIC-MS Seminars:
ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. With this project we want to provide a centralized web platform for both developers and end-users to allow for an easy and controlled comparison of proteomics data analysis workflows. The goal is not to select a single best one-fits-all data analysis workflow, but to allow:
- End-users to identify a good workflow to fulfill their specific needs
- Developers to identify the specific strengths and weaknesses in their workflows, guiding the development process
- The field to easily position a newly published workflow within the context of the existing state-of-the-art
Rusteomics is an open and collaborative community for Rust development for computational proteomics and mass spectrometry.
Recently, the Rust programming language has been steadily gaining popularity, mostly due to its high performance as a low-level language and its developer-friendly toolchain. Furthermore, Rust is compatible with all major operating systems, and bindings can be created to extend its functionality to other programming languages, such as Python or R. These characteristics provide a unique opportunity for computational proteomics developers to unite and collaborate on a new open and flexible toolbox for computational proteomics and mass spectrometry.
The aim of Rusteomics is to facilitate the development of such a community-driven toolbox in an open and transparent manner. It spawned as a project of the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) and was kickstarted as a hackathon at the EuBIC-MS Developers Meeting 2023.
Proteomics Sample Data Relationship Format (SDRF)
Metadata is essential in proteomics data repositories and is crucial to interpret and reanalyze the deposited data sets. While the dataset general description and standard data file formats are supported and captured for every dataset by ProteomeXchange partners, the information regarding the sample to data files is mostly missing. Recently, the members of the EuBIC-MS have created this open-source project to enable the standardization of sample metadata of public proteomics data sets. Further development of SDRF is organized jointly between EuBIC-MS and HUPO-PSI.
EuBIC-MS Guidelines for Reproducible MS-based Experiments
This project aims at defining a set of guidelines to report mass spectrometry-based experiments in a reproducible fashion.
There is a growing concern about a lack of reproducibility in science that also affects bioinformatics and mass spectrometry (MS-based) technologies. One aspect of this problem is that bioinformatic analysis are increasingly complex and greatly influence the outcome of a study. Current bioinformatic analysis commonly consist of multiple tools and algorithms, each with its own set of parameters. Recording all of these settings in full detail is rarely possible in methods sections of a research manuscript. This often leads to vital details about the bioinformatic processing of the data to be missing. In this work, we, therefore, try to establish a set of guidelines to describe:
- The minimal information required in the bioinformatic methods section of MS-based manuscripts.
- A well-defined checklist of requirements to help authors, reviewers, and editors to assess bioinformatic analyses
- The required extended information data (supplementary) that needs to accompany any manuscript in order to ensure its reproducibility
Proteomics Academy is a joint effort of the European Proteomics Association (EuPA) educational committee and EuBIC-MS. Its aim is to foster interaction between scientists interested in proteomics in an open, constructive, and collaborative way. We will be happy to answer your questions, receive your suggestions, and we welcome anyone wanting to join this community effort. Proteomics Academy bundles together a Q&A forum, online educational material, and much more!