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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References
Matthiesen R, Azevedo L, Amorim A et al (2011) Discussion on common data analysis strategies used in MS-based proteomics. Proteomics 11(4):604–619. https://doi.org/10.1002/pmic.201000404
Schjoldager KT, Narimatsu Y, Joshi HJ et al (2020) Global view of human protein glycosylation pathways and functions. Nat Rev Mol Cell Biol 21(12):729–749. https://doi.org/10.1038/s41580-020-00294-x
Swatek KN, Komander D (2016) Ubiquitin modifications. Cell Res 26(4):399–422. https://doi.org/10.1038/cr.2016.39
Bedford L, Lowe J, Dick LR et al (2011) Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug targets. Nat Rev Drug Discov 10(1):29–46. https://doi.org/10.1038/nrd3321
Quinet G, Xolalpa W, Reyes-Garau D et al (2022) Constitutive activation of p62/Sequestosome-1-mediated Proteaphagy regulates proteolysis and impairs cell death in Bortezomib-resistant mantle cell lymphoma. Cancers 14(4):doi:10.3390/cancers14040923
Mata-Cantero L, Azkargorta M, Aillet F et al (2016) New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach. J Proteome 139:45–59. https://doi.org/10.1016/j.jprot.2016.03.004
Lopitz-Otsoa F, Rodriguez-Suarez E, Aillet F et al (2012) Integrative analysis of the ubiquitin proteome isolated using tandem ubiquitin binding entities (TUBEs). J Proteome 75(10):2998–3014. https://doi.org/10.1016/j.jprot.2011.12.001
Hjerpe R, Aillet F, Lopitz-Otsoa F et al (2009) Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. EMBO Rep 10(11):1250–1258. https://doi.org/10.1038/embor.2009.192
Akimov V, Barrio-Hernandez I, Hansen SVF et al (2018) UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites. Nat Struct Mol Biol 25(7):631–640. https://doi.org/10.1038/s41594-018-0084-y
Lee KA, Hammerle LP, Andrews PS et al (2011) Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. J Biol Chem 286(48):41530–41538. https://doi.org/10.1074/jbc.M111.248856
Pirone L, Xolalpa W, Sigurethsson JO et al (2017) A comprehensive platform for the analysis of ubiquitin-like protein modifications using in vivo biotinylation. Sci Rep 7:40756. https://doi.org/10.1038/srep40756
Trulsson F, Akimov V, Robu M et al (2022) Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates. Nat Commun 13(1):2736. https://doi.org/10.1038/s41467-022-30376-7
Tyanova S, Temu T, Cox J (2016) The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11(12):2301–2319. https://doi.org/10.1038/nprot.2016.136
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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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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