Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes. These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR's existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper.

Analytical Biochemistry Department of Pharmacy University of Groningen Groningen 9713 AV Netherlands

Applied Bio and Molecular Systems VITO Mol BE 2400 Belgium

Applied Bioinformatics Department of Computer Science University of Tübingen Tübingen 72074 Germany

Biomolecular Interactions Max Planck Institute for Developmental Biology Tübingen 72076 Germany

Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences University of Utrecht Utrecht 3548 CH Netherlands

CALIPHO Group SIB Swiss Institute of Bioinformatics Geneva 1015 Switzerland

Center for Bioinformatics Tübingen University of Tübingen Tübingen 72074 Germany

Center for Biotechnology Bielefeld University Bielefeld 33615 Germany

Center for Proteomics and Metabolomics Leiden University Medical Center Leiden 2333 ZA Netherlands

Center for Proteomics University of Antwerp Antwerpen 2000 Belgium

Computer Science Department University of Geneva Geneva 1205 Switzerland

Department of Biochemistry and Molecular Biology University of Southern Denmark Odense M 5230 Denmark

Department of Biochemistry Ghent University Ghent 9000 Belgium

Department of Biomedical Sciences University of Padova Padova 1 35121 Italy

Department of Human Protein Science Faculty of Medicine University of Geneva Geneva 1205 Switzerland

Department of Mathematics and Computer Science University of Antwerp Antwerp 2020 Belgium

Dutch Techcentre for Life Sciences ELIXIR NL Utrecht 3511 GC Netherlands

ELIXIR Hub Cambridge CB10 1SD UK

European Molecular Biology Laboratory European Bioinformatics Institute Cambridge CB10 1SD UK

French Proteomics Infrastructure ProFI Grenoble France

Institute of Microbiology Czech Academy of Sciences Prague 1 117 20 Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague 1 117 20 Czech Republic

Interuniversity Institute for Biostatistics and Statistical Bioinformatics Hasselt University Hasselt 3500 Belgium

Medical Bioinformatics Medizinisches Proteom Center Ruhr University Bochum Bochum 44801 Germany

National Bioinformatics Infrastructure Sweden SciLifeLab Department of Immunotechnology Lund University Lund 223 62 Sweden

Netherlands Metabolomics Centre Utrecht 3511 GC Netherlands

Netherlands Proteomics Center Utretcht 3584 CH Netherlands

Proteome Informatics Group SIB Swiss Institute of Bioinformatics Geneva 1015 Switzerland

ProteoRed Proteomics Unit Centro Nacional de Biotecnología Madrid 28049 Spain

Quantitative Biology Center University of Tübingen Tübingen 72074 Germany

VIB UGent Center for Medical Biotechnology Ghent 9052 Belgium

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Mallick P, Kuster B: Proteomics: a pragmatic perspective. Nat Biotechnol. 2010;28(7):695–709. 10.1038/nbt.1658 PubMed DOI

Aebersold R, Mann M: Mass-spectrometric exploration of proteome structure and function. Nature. 2016;537(7620):347–55. 10.1038/nature19949 PubMed DOI

Menschaert G, Fenyö D: Proteogenomics from a bioinformatics angle: A growing field. Mass Spectrom Rev. 2015. 10.1002/mas.21483 PubMed DOI PMC

Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–72. 10.1038/nbt.1511 PubMed DOI

Röst HL, Sachsenberg T, Aiche S, et al. : OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016;13(9):741–8. 10.1038/nmeth.3959 PubMed DOI

Barsnes H, Vaudel M, Colaert N, et al. : compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics. 2011;12:70. 10.1186/1471-2105-12-70 PubMed DOI PMC

Vaudel M, Burkhart JM, Zahedi RP, et al. : PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol. 2015;33(1):22–4. 10.1038/nbt.3109 PubMed DOI

Vizcaino JA, Csordas A, del-Toro N, et al. : 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44(D1):D447–56. 10.1093/nar/gkv1145 PubMed DOI PMC

Deutsch EW, Csordas A, Sun Z, et al. : The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 2017;45(D1):D1100–D6. 10.1093/nar/gkw936 PubMed DOI PMC

Deutsch EW, Albar JP, Binz PA, et al. : Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc. 2015;22(3):495–506. 10.1093/jamia/ocv001 PubMed DOI PMC

Uhlén M, Fagerberg L, Hallström BM, et al. : Proteomics. Tissue-based map of the human proteome. Science. 2015;347(6220):1260419. 10.1126/science.1260419 PubMed DOI

UniProt Consortium: UniProt: a hub for protein information. Nucleic Acids Res. 2015;43(Database issue):D204–12. 10.1093/nar/gku989 PubMed DOI PMC

Lane L, Argoud-Puy G, Britan A, et al. : neXtProt: a knowledge platform for human proteins. Nucleic Acids Res. 2012;40(Database issue):D76–83. 10.1093/nar/gkr1179 PubMed DOI PMC

Martens L, Vizcaíno JA: A Golden Age for Working with Public Proteomics Data. Trends Biochem Sci. 2017;42(5):333–341. 10.1016/j.tibs.2017.01.001 PubMed DOI PMC

Ison J, Rapacki K, Ménager H, et al. : Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2016;44(D1):D38–47. 10.1093/nar/gkv1116 PubMed DOI PMC

Willems S, Bouyssié D, David M, et al. : Proceedings of the EuBIC Winter School 2017. J Proteomics. 2017;161:78–80. 10.1016/j.jprot.2017.04.001 PubMed DOI

Durinx C, McEntyre J, Appel R, et al. : Identifying ELIXIR Core Data Resources [version 2; referees: 2 approved]. F1000Res. 2016;5: pii: ELIXIR-2422. 10.12688/f1000research.9656.2 PubMed DOI PMC

Eijssen L, Evelo C, Kok R, et al. : The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands [version 2; referees: 2 approved, 1 approved with reservations]. F1000Res. 2015;4:33. 10.12688/f1000research.6009.2 PubMed DOI PMC

Wilkinson MD, Dumontier M, Aalbersberg IJ, et al. : The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018. 10.1038/sdata.2016.18 PubMed DOI PMC

Smith LM, Kelleher NL, Consortium for Top Down Proteomics : Proteoform: a single term describing protein complexity. Nat Methods. 2013;10(3):186–7. 10.1038/nmeth.2369 PubMed DOI PMC

Vaudel M, Verheggen K, Csordas A, et al. : Exploring the potential of public proteomics data. Proteomics. 2016;16(2):214–25. 10.1002/pmic.201500295 PubMed DOI PMC

Robertsen EM, Denise H, Mitchell A, et al. : ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services [version 1; referees: 1 approved, 2 approved with reservations]. F1000Res. 2017;6: (ELIXIR)(70). 10.12688/f1000research.10443.1 PubMed DOI PMC