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Whilst the pivotal role of skeletal muscle in overall health is widely acknowledged, unravelling the underlying molecular mechanisms poses ongoing challenges. Protein ubiquitylation, a crucial post\u2010translational modification, is involved in regulating most biological processes. This widespread impact is achieved through a diverse set of enzymes capable of generating structurally and functionally distinct ubiquitin modifications on proteins. The complexity of protein ubiquitylation has presented significant challenges in not only identifying ubiquitylated proteins but also characterising their functional significance. Mass spectrometry enables in\u2010depth analysis of proteins and their post\u2010translational modification status, offering a powerful tool for studying protein ubiquitylation and its biological diversity: an approach termed ubiquitylomics. Ubiquitylomics has been employed to tackle different perspectives of ubiquitylation, including but not limited to global quantification of substrates and ubiquitin linkages, ubiquitin site recognition and crosstalk with other post\u2010translational modifications. As the field of mass spectrometry continues to evolve, the usage of ubiquitylomics has unravelled novel insights into the regulatory mechanisms of protein ubiquitylation governing biology. However, ubiquitylomics research has predominantly been conducted in cellular models, limiting our understanding of ubiquitin signalling events driving skeletal muscle biology. By integrating the intricate landscape of protein ubiquitylation with dynamic shifts in muscle physiology, ubiquitylomics promises to not only deepen our understanding of skeletal muscle biology but also lay the foundation for developing transformative muscle\u2010related therapeutics. This review aims to articulate how ubiquitylomics can be utilised by researchers to address different aspects of ubiquitylation signalling in skeletal muscle. We explore methods used in ubiquitylomics experiments, highlight relevant literature employing ubiquitylomics in the context of skeletal muscle and outline considerations for experimental design.<\/jats:p>","DOI":"10.1002\/jcsm.13601","type":"journal-article","created":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T09:29:20Z","timestamp":1726478960000},"page":"2281-2294","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Ubiquitylomics: An Emerging Approach for Profiling Protein Ubiquitylation in Skeletal Muscle"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6241-7966","authenticated-orcid":false,"given":"Samuel\u00a0O.","family":"Lord","sequence":"first","affiliation":[{"name":"School of Sport, Exercise and Rehabilitation Sciences University of Birmingham  Birmingham UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7032-0227","authenticated-orcid":false,"given":"Harvey\u00a0E.","family":"Johnston","sequence":"additional","affiliation":[{"name":"Signalling Programme The Babraham Institute  Cambridge UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1952-259X","authenticated-orcid":false,"given":"Rahul\u00a0S.","family":"Samant","sequence":"additional","affiliation":[{"name":"Signalling Programme The Babraham Institute  Cambridge UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8254-3732","authenticated-orcid":false,"given":"Yu\u2010Chiang","family":"Lai","sequence":"additional","affiliation":[{"name":"School of Sport, Exercise and Rehabilitation Sciences University of Birmingham  Birmingham UK"},{"name":"MRC Versus Arthritis Centre for Musculoskeletal Ageing Research University of Birmingham  Birmingham UK"},{"name":"NIHR Birmingham Biomedical Research Centre Sarcopenia and Multimorbidity University of Birmingham  Birmingham UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,9,16]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2007.11.003"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcsm.13263"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1249\/MSS.0000000000000975"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00223-018-0478-1"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.67.1.425"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-03060-1"},{"key":"e_1_2_12_8_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmolb.2022.1008175","article-title":"Non\u2010Lysine Ubiquitylation: Doing Things Differently","volume":"9","author":"Kelsall I. 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