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A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples

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The Ubiquitin Code

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2602))

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Abstract

Mass spectrometry data on ubiquitin and ubiquitin-like modifiers are becoming increasingly more accessible, and the coverage progressively deepen as methodologies mature. This type of mass spectrometry data is linked to specific data analysis pipelines for ubiquitin. This chapter describes a computational tool to facilitate analysis of mass spectrometry data obtained on ubiquitin-enriched samples. For example, the analysis of ubiquitin branch site statistics and functional enrichment analysis against ubiquitin proteasome system protein sets are completed with a few functional calls. We foresee that the proposed computational methodology can aid in proximity drug design by, for example, elucidating the expression of E3 ligases and other factors related to the ubiquitin proteasome system.

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Acknowledgments

R.M. is supported by Fundação para a Ciência e a Tecnologia (CEEC position, 2019–2025 investigator). This article is a result of the projects (iNOVA4Health—UIDB/04462/2020), supported by Lisboa Portugal Regional Operational Programme (Lisboa, 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). This work is also funded by FEDER funds through the COMPETE 2020 Programme and National Funds through FCT—Portuguese Foundation for Science and Technology under the projects number PTDC/BTM-TEC/30087/2017 and PTDC/BTM-TEC/30088/2017. This publication is based upon work from COST Action, CA20113 “PROTEOCURE” supported by COST (European Cooperation in Science and Technology).

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Authors and Affiliations

  1. iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, Lisbon, Portugal

    Rune Matthiesen & Ana Sofia Carvalho

  2. Laboratoire de Chimie de Coordination (LCC)-CNRS, UPS, Toulouse, France

    Manuel S. Rodriguez

Authors
  1. Rune Matthiesen
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  2. Manuel S. Rodriguez
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  3. Ana Sofia Carvalho
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Corresponding author

Correspondence to Rune Matthiesen .

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Editors and Affiliations

  1. LCC-UPR 8241-CNRS Equipe M, Laboratoire de Chimie de Coordination, Toulouse, France

    Manuel S Rodriguez

  2. CIC bioGUNE, Derio, Spain

    Rosa Barrio

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Matthiesen, R., Rodriguez, M.S., Carvalho, A.S. (2023). A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples. In: Rodriguez, M.S., Barrio, R. (eds) The Ubiquitin Code. Methods in Molecular Biology, vol 2602. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2859-1_15

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  • DOI: https://doi.org/10.1007/978-1-0716-2859-1_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2858-4

  • Online ISBN: 978-1-0716-2859-1

  • eBook Packages: Springer Protocols

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