ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics

ChemRxiv

Abstract

Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and complexity between raw and machine learning-ready formats. While predictive proteomics is a field on the rise, when predicting peptide behavior in LC-IM-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility. For this reason we introduce ProteomicsML, an online resource for proteomics-based datasets and tutorials across most of the currently explored physicochemical peptide properties. This community-driven resource makes it simple to access data in easy-to-process formats, and contains easy-to-follow tutorials that allow new users to interact with even the most advanced algorithms in the field. ProteomicsML provides datasets that are useful for comparing state-of-the-art (SOTA) machine learning algorithms, as well as providing introductory material for teachers and newcomers to the field alike. The platform is freely available on https://www.proteomicsml.org/ and we welcome the entire proteomics community to contribute to the project at https://github.com/proteomicsml/.

Authors 10

1. Tobias Greisager Rehfeldt

   University of Southern Denmark

   Affiliation as printed

   University of Southern Denmark

2. Ralf Gabriels

   Ghent University

   Affiliation as printed

   Ghent University

3. Robbin Bouwmeester

   Ghent University

   Affiliation as printed

   Ghent University

4. Siegfried Gessulat
   Affiliation as printed

   MSAID Gmbh

5. Benjamin A. Neely

   National Institute of Standards and Technology

   Affiliation as printed

   National Institute of Standards and Technology

6. Magnus Palmblad Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

7. Yasset Pérez‐Riverol

   European Bioinformatics Institute

   Affiliation as printed

   European Bioinformatics Institute

8. Tobias F. N. Schmidt
   Affiliation as printed

   MSAID Gmbh

   MSAID GmbH

9. Juan Antonio Vizcaíno

   European Bioinformatics Institute

   Affiliation as printed

   European Bioinformatics Institute

10. Eric W. Deutsch

    Institute for Systems Biology

    Affiliation as printed

    Institute for Systems Biology