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Toward an Integrated Machine Learning Model of a Proteomics Experiment

Neely, Benjamin A. (author)
National Institute of Standards and Technology, Charleston, South Carolina 29412, United States
Dorfer, Viktoria (author)
Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria, Softwarepark 11
Martens, Lennart (author)
VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
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Bludau, Isabell (author)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
Bouwmeester, Robbin (author)
VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
Degroeve, Sven (author)
VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
Deutsch, Eric W. (author)
Institute for Systems Biology, Seattle, Washington 98109, United States
Gessulat, Siegfried (author)
MSAID GmbH, 10559 Berlin, Germany
Käll, Lukas, 1969- (author)
KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
Palczynski, Pawel (author)
Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
Payne, Samuel H. (author)
Department of Biology, Brigham Young University, Provo, Utah 84602, United States
Rehfeldt, Tobias Greisager (author)
Institute for Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
Schmidt, Tobias (author)
MSAID GmbH, 85748 Garching, Germany
Schwämmle, Veit (author)
Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
Uszkoreit, Julian (author)
Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany; Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany
Vizcaíno, Juan Antonio (author)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom, Cambridge
Wilhelm, Mathias (author)
Computational Mass Spectrometry, Technical University of Munich (TUM), 85354 Freising, Germany
Palmblad, Magnus (author)
Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands, Postbus 9600
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 (creator_code:org_t)
2023-02-06
2023
English.
In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 22:3, s. 681-696
Related links:
https://doi.org/10.1...
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https://urn.kb.se/re...
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  • Research review (peer-reviewed)
Abstract Subject headings
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  • In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and explore machine learning applications for realistic modeling of data from multidimensional mass spectrometry-based proteomics analysis of any sample or organism. Following this sample-to-data roadmap helped identify knowledge gaps and define needs. Being able to generate bespoke and realistic synthetic data has legitimate and important uses in system suitability, method development, and algorithm benchmarking, while also posing critical ethical questions. The interdisciplinary nature of the workshop informed discussions of what is currently possible and future opportunities and challenges. In the following perspective we summarize these discussions in the hope of conveying our excitement about the potential of machine learning in proteomics and to inspire future research.

Subject headings

NATURVETENSKAP  -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
NATURAL SCIENCES  -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

Keyword

artificial intelligence
deep learning
enzymatic digestion
ion mobility
liquid chromatography
machine learning
research integrity
synthetic data
tandem mass spectrometry

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