The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS; eubic-ms.org) was founded in 2014 to unite European computational mass spectrometry researchers and proteomics bioinformaticians working in academia and industry. EuBIC-MS maintains educational resources (proteomics-academy.org) and organises workshops at national and international conferences on proteomics and mass spectrometry. Furthermore, EuBIC-MS is actively involved in several community initiatives such as the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Apart from these collaborations, EuBIC-MS has organised two Winter Schools and two Developers' Meetings that have contributed to the strengthening of the European mass spectrometry network and fostered international collaboration in this field, even beyond Europe. Moreover, EuBIC-MS is currently actively developing a community-driven standard dedicated to mass spectrometry data annotation (SDRF-Proteomics) that will facilitate data reuse and collaboration. This manuscript highlights what EuBIC-MS is, what it does, and what it already has achieved. A warm invitation is extended to new researchers at all career stages to join the EuBIC-MS community on its Slack channel (eubic.slack.com).
- 1, , , et al. Proceedings of the EuBIC Winter School 2017. J Proteomics. 2017; 161: 78-80.
- 2, , , et al. Proceedings of the EuBIC Winter School 2019. EuPA Open Proteom. 2019; 22–23: 4-7.
- 3, , , et al. Proceedings of the EuBIC Developer's Meeting 2018. J Proteomics. 2018; 187: 25-27.
- 4, , , et al. Proceedings of the EuBIC-MS 2020 Developers' Meeting. EuPA Open Proteom. 2020; 24: 1-6.
- 5, , , et al. qcML: An exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014; 13(8): 1905-1913.
- 6, , , , , . QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Anal Chem. 2014; 86(5): 2497-2509.
- 7, , , et al. OpenMS: A flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016; 13(9): 741-748.
- 8 The M, . MaRaCluster: A fragment rarity metric for clustering fragment spectra in shotgun proteomics. J Proteome Res. 2016; 15(3): 713-720.
- 9, , . IsoProt: A complete and reproducible workflow to analyze iTRAQ/TMT experiments. J Proteome Res. 2019; 18(4): 1751-1759.
- 10, , , et al. ThermoRawFileParser: Modular, scalable, and cross-platform RAW file conversion. J Proteome Res. 2020; 19(1): 537-542.
- 11, , , et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11): 2498-2504.
- 12, , , et al. MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets. J Proteome Res. 2021; 20(4): 2083–2088. https://doi.org/10.1021/acs.jproteome.0c00926
- 13, , , et al. Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison. bioRxiv. 2020. https://doi.org/10.1101/2020.09.08.287557
- 14, , , et al. Universal Spectrum Identifier for mass spectra. bioRxiv. 2020. https://doi.org/10.1101/2020.12.07.415539
- 15, , , et al. A community proposal to integrate proteomics activities in ELIXIR. F1000Res. 2017; 6: 875.
- 16, , , et al. The PRIDE database and related tools and resources in 2019: Improving support for quantification data. Nucleic Acids Res. 2019; 47(D1): D442-D450.
- 17, , , et al. Proteomics standards initiative: Fifteen years of progress and future work. J Proteome Res. 2017; 16(12): 4288-4298.
- 18, , , et al. mzML – a community standard for mass spectrometry data. Mol Cell Proteomics. 2011; 10(1):R110-000133.
- 19, , , et al. Proteomics standards initiative extended FASTA format. J Proteome Res. 2019; 18(6): 2686-2692.
- 20, European Bioinformatics Community for Mass Spectrometry. Toward a sample metadata standard in public proteomics repositories. J Proteome Res. 2020; 19(10): 3906-3909.
- 21, , , et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinf. 2006; 7(1):365.
- 22, , , et al. The ProteomeXchange consortium in 2017: Supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 2017; 45(D1): D1100-D1106.