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 EuBIC-MS Developer’s 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.
The previous EuBIC-MS Developer’s Meeting took place from January 13th – 17th 2020 in Nyborg, Denmark.
The EuBIC-MS Internal Meetings are used to host a series of talks or workshops. This is an opportunity to exchange on current projects of EuBIC-MS members in a friendly and open atmosphere.
The first series took place in Copenhagen to take place on the 6th October 2021.
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.
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!