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As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations\/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic\/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.<\/jats:p>","DOI":"10.3390\/proteomes12010004","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T11:37:18Z","timestamp":1705405038000},"page":"4","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9290-9267","authenticated-orcid":false,"given":"Paul","family":"Dowling","sequence":"first","affiliation":[{"name":"Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland"},{"name":"Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Capucine","family":"Trollet","sequence":"additional","affiliation":[{"name":"Center for Research in Myology U974, Sorbonne Universit\u00e9, INSERM, Myology Institute, 75013 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elisa","family":"Negroni","sequence":"additional","affiliation":[{"name":"Center for Research in Myology U974, Sorbonne Universit\u00e9, INSERM, Myology Institute, 75013 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0923-7090","authenticated-orcid":false,"given":"Dieter","family":"Swandulla","sequence":"additional","affiliation":[{"name":"Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6266-4510","authenticated-orcid":false,"given":"Kay","family":"Ohlendieck","sequence":"additional","affiliation":[{"name":"Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. 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PLoS Biol., 14.","DOI":"10.1101\/036103"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e2303077120","DOI":"10.1073\/pnas.2303077120","article-title":"The human cell count and size distribution","volume":"120","author":"Hatton","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.cels.2017.12.004","article-title":"Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome","volume":"6","author":"Ho","year":"2018","journal-title":"Cell Syst."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5301","DOI":"10.1038\/s41467-020-19045-9","article-title":"A high-stringency blueprint of the human proteome","volume":"11","author":"Adhikari","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.cell.2020.08.036","article-title":"A Quantitative Proteome Map of the Human Body","volume":"183","author":"Jiang","year":"2020","journal-title":"Cell"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4735","DOI":"10.1021\/acs.jproteome.0c00485","article-title":"Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project","volume":"19","author":"Omenn","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Pertea, M., and Salzberg, S.L. (2010). Between a chicken and a grape: Estimating the number of human genes. Genome Biol., 11.","DOI":"10.1186\/gb-2010-11-5-206"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41586-023-06490-x","article-title":"The status of the human gene catalogue","volume":"622","author":"Amaral","year":"2023","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nmeth.2369","article-title":"Proteoform: A single term describing protein complexity","volume":"10","author":"Smith","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nchembio.2576","article-title":"How many human proteoforms are there?","volume":"14","author":"Aebersold","year":"2018","journal-title":"Nat. Chem. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e1800361","DOI":"10.1002\/pmic.201800361","article-title":"Identification and Quantification of Proteoforms by Mass Spectrometry","volume":"19","author":"Schaffer","year":"2019","journal-title":"Proteomics"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Carbonara, K., Andonovski, M., and Coorssen, J.R. (2021). Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes, 9.","DOI":"10.3390\/proteomes9030038"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e00260","DOI":"10.1016\/j.plabm.2021.e00260","article-title":"Proteoforms and their expanding role in laboratory medicine","volume":"28","author":"Forgrave","year":"2021","journal-title":"Pract. Lab. Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"eabk0734","DOI":"10.1126\/sciadv.abk0734","article-title":"The Human Proteoform Project: Defining the human proteome","volume":"7","author":"Smith","year":"2021","journal-title":"Sci. Adv."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1080\/14789450.2017.1364996","article-title":"Mapping the human skeletal muscle proteome: Progress and potential","volume":"14","author":"Capitanio","year":"2017","journal-title":"Expert Rev. Proteom."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/jcsm.12121","article-title":"The Human Skeletal Muscle Proteome Project: A reappraisal of the current literature","volume":"8","author":"Semba","year":"2017","journal-title":"J. Cachexia Sarcopenia Muscle"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1080\/14789450.2020.1879647","article-title":"The application of proteomics in muscle exercise physiology","volume":"17","author":"Hesketh","year":"2020","journal-title":"Expert Rev. Proteom."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/s41580-021-00389-z","article-title":"Molecular and cellular basis of genetically inherited skeletal muscle disorders","volume":"22","author":"Dowling","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/S1474-4422(20)30028-4","article-title":"Advances in the diagnosis of inherited neuromuscular diseases and implications for therapy development","volume":"19","author":"Thompson","year":"2020","journal-title":"Lancet Neurol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s41572-021-00248-3","article-title":"Duchenne muscular dystrophy","volume":"7","author":"Duan","year":"2021","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1183101","DOI":"10.3389\/fphys.2023.1183101","article-title":"Duchenne muscular dystrophy: Disease mechanism and therapeutic strategies","volume":"14","author":"Hosny","year":"2023","journal-title":"Front. Physiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3879","DOI":"10.1111\/febs.15466","article-title":"The discovery of dystrophin, the protein product of the Duchenne muscular dystrophy gene","volume":"287","author":"Hoffman","year":"2020","journal-title":"FEBS J."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/S0065-2660(08)60334-X","article-title":"Dystrophin, its gene, and the dystrophinopathies","volume":"33","author":"Roberts","year":"1995","journal-title":"Adv. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1016\/j.nmd.2021.08.004","article-title":"The DMD gene and therapeutic approaches to restore dystrophin","volume":"31","author":"Fortunato","year":"2021","journal-title":"Neuromuscul. Disord."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1016\/S0140-6736(19)32910-1","article-title":"Muscular dystrophies","volume":"394","author":"Mercuri","year":"2019","journal-title":"Lancet"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/S1474-4422(18)30024-3","article-title":"Diagnosis and management of Duchenne muscular dystrophy, part 1: Diagnosis, and neuromuscular, rehabilitation, endocrine, and gastrointestinal and nutritional management","volume":"17","author":"Birnkrant","year":"2018","journal-title":"Lancet Neurol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/S1474-4422(18)30025-5","article-title":"Diagnosis and management of Duchenne muscular dystrophy, part 2: Respiratory, cardiac, bone health, and orthopaedic management","volume":"17","author":"Birnkrant","year":"2018","journal-title":"Lancet Neurol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S1474-4422(18)30026-7","article-title":"Diagnosis and management of Duchenne muscular dystrophy, part 3: Primary care, emergency management, psychosocial care, and transitions of care across the lifespan","volume":"17","author":"Birnkrant","year":"2018","journal-title":"Lancet Neurol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1136\/archdischild-2014-307962","article-title":"Recent advances in the management of Duchenne muscular dystrophy","volume":"100","author":"Strehle","year":"2015","journal-title":"Arch. Dis. Child."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1007\/s10072-018-3555-3","article-title":"Clinical management of Duchenne muscular dystrophy: The state of the art","volume":"39","author":"Messina","year":"2018","journal-title":"Neurol. Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1007\/s00424-021-02623-1","article-title":"Complexity of skeletal muscle degeneration: Multi-systems pathophysiology and organ crosstalk in dystrophinopathy","volume":"473","author":"Ohlendieck","year":"2021","journal-title":"Pflugers Arch."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.molcel.2021.12.012","article-title":"New horizons in the stormy sea of multimodal single-cell data integration","volume":"82","author":"Jackson","year":"2022","journal-title":"Mol. Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1152\/physiolgenomics.00292.2007","article-title":"Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry","volume":"33","author":"Mirza","year":"2008","journal-title":"Physiol. Genom."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1146\/annurev-genom-112921-024948","article-title":"Obtaining Complete Human Proteomes","volume":"23","author":"Olsen","year":"2022","journal-title":"Annu. Rev. Genom. Hum. Genet."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1002\/elps.1150170329","article-title":"Characterisation of proteins from two-dimensional electrophoresis gels by matrix-assisted laser desorption mass spectrometry and amino acid compositional analysis","volume":"17","author":"Wheeler","year":"1996","journal-title":"Electrophoresis"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1080\/02648725.1996.10647923","article-title":"Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it","volume":"13","author":"Wilkins","year":"1996","journal-title":"Biotechnol. Genet. Eng. Rev."},{"key":"ref_41","first-page":"61","article-title":"From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis","volume":"14","author":"Wilkins","year":"1996","journal-title":"Biotechnology"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.tibs.2021.01.013","article-title":"Single-Cell Proteomics","volume":"46","author":"Vistain","year":"2021","journal-title":"Trends Biochem. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2335","DOI":"10.1016\/j.molcel.2022.05.022","article-title":"Unbiased spatial proteomics with single-cell resolution in tissues","volume":"82","author":"Mund","year":"2022","journal-title":"Mol. Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e2200162","DOI":"10.1002\/pmic.202200162","article-title":"Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing","volume":"23","author":"Matzinger","year":"2023","journal-title":"Proteomics"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1042\/EBC20220098","article-title":"Seeing the complete picture: Proteins in top-down mass spectrometry","volume":"67","author":"Habeck","year":"2023","journal-title":"Essays Biochem."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1039\/D2AN01246D","article-title":"Overview and considerations in bottom-up proteomics","volume":"148","author":"Miller","year":"2023","journal-title":"Analyst"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1007\/s13361-019-02201-x","article-title":"Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches","volume":"30","author":"Lermyte","year":"2019","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Dowling, P., Swandulla, S., and Ohlendieck, K. (2023). Mass spectrometry-based proteomic technology and its application to study skeletal muscle cell biology. Cells, 12.","DOI":"10.3390\/cells12212560"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Dowling, P., Gargan, S., Swandulla, D., and Ohlendieck, K. (2023). Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24032415"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1080\/14789450.2023.2255743","article-title":"Biochemical and proteomic insights into sarcoplasmic reticulum Ca2+-ATPase complexes in skeletal muscles","volume":"20","author":"Dowling","year":"2023","journal-title":"Expert Rev. Proteom."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"351","DOI":"10.12688\/f1000research.16987.1","article-title":"Recent technical advances in proteomics","volume":"8","author":"Yates","year":"2019","journal-title":"F1000Research"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/978-1-4939-9744-2_7","article-title":"Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry","volume":"2051","author":"Matthiesen","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-1-0716-1024-4_8","article-title":"Quantitative Mass Spectrometry-Based Proteomics: An Overview","volume":"2228","author":"Rozanova","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Neagu, A.N., Jayathirtha, M., Baxter, E., Donnelly, M., Petre, B.A., and Darie, C.C. (2022). Applications of Tandem Mass Spectrometry (MS\/MS) in Protein Analysis for Biomedical Research. Molecules, 27.","DOI":"10.3390\/molecules27082411"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.jprot.2014.03.035","article-title":"2DE: The phoenix of proteomics","volume":"104","author":"Oliveira","year":"2014","journal-title":"J. Proteom."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1080\/13813455.2016.1179766","article-title":"2D gel-based Proteomics: There\u2019s life in the old dog yet","volume":"122","author":"Westermeier","year":"2016","journal-title":"Arch. Physiol. Biochem."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Zhan, X., Li, B., Zhan, X., Schl\u00fcter, H., Jungblut, P.R., and Coorssen, J.R. (2019). Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level. Proteomes, 7.","DOI":"10.3390\/proteomes7040036"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Marcus, K., Lelong, C., and Rabilloud, T. (2020). What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?. Proteomes, 8.","DOI":"10.3390\/proteomes8030017"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Murphy, S., Dowling, P., and Ohlendieck, K. (2016). Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis. Proteomes, 4.","DOI":"10.3390\/proteomes4030027"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Dowling, P., Zweyer, M., Swandulla, D., and Ohlendieck, K. (2019). Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes, 7.","DOI":"10.3390\/proteomes7020025"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/978-1-59745-281-6_20","article-title":"High-resolution large-gel 2DE","volume":"519","author":"Zabel","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/S0076-6879(09)63030-5","article-title":"Isoelectric focusing and two-dimensional gel electrophoresis","volume":"463","author":"Friedman","year":"2009","journal-title":"Methods Enzymol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2064","DOI":"10.1016\/j.jprot.2010.05.016","article-title":"Two-dimensional gel electrophoresis in proteomics: Past, present and future","volume":"73","author":"Rabilloud","year":"2010","journal-title":"J. Proteom."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1016\/j.jprot.2011.05.040","article-title":"Two-dimensional gel electrophoresis in proteomics: A tutorial","volume":"74","author":"Rabilloud","year":"2011","journal-title":"J. Proteom."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"168","DOI":"10.3109\/13813455.2014.945188","article-title":"Looking at proteins from two dimensions: A review on five decades of 2D electrophoresis","volume":"120","author":"Westermeier","year":"2014","journal-title":"Arch. Physiol. Biochem."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"460763","DOI":"10.1016\/j.chroma.2019.460763","article-title":"The evolution of two-dimensional gel electrophoresis\u2014From proteomics to emerging alternative applications","volume":"1615","author":"Lee","year":"2020","journal-title":"J. Chromatogr. A"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-60327-834-8_1","article-title":"A high-resolution two dimensional Gel- and Pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling","volume":"527","author":"Agrawal","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.redox.2015.05.006","article-title":"Oxidative proteome alterations during skeletal muscle ageing","volume":"5","author":"Baraibar","year":"2015","journal-title":"Redox Biol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Rodr\u00edguez-V\u00e1zquez, R., Mouzo, D., and Zapata, C. (2022). Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation. Foods, 11.","DOI":"10.3390\/foods11193119"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-59745-493-3_4","article-title":"Classical proteomics: Two-dimensional electrophoresis\/MALDI mass spectrometry","volume":"492","author":"Schmid","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1002\/elps.201100642","article-title":"Optimization of large gel 2D electrophoresis for proteomic studies of skeletal muscle","volume":"33","author":"Reed","year":"2012","journal-title":"Electrophoresis"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ab.2018.05.012","article-title":"Coomassie does it (better): A Robin Hood approach to total protein quantification","volume":"556","author":"Noaman","year":"2018","journal-title":"Anal. Biochem."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"3086","DOI":"10.1002\/elps.201700190","article-title":"Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics","volume":"38","author":"Noaman","year":"2017","journal-title":"Electrophoresis"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"4784","DOI":"10.3390\/ma3104784","article-title":"Standard Dyes for Total Protein Staining in Gel-Based Proteomic Analysis","volume":"3","author":"Chevalier","year":"2010","journal-title":"Materials"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1586\/epr.12.63","article-title":"A blue dive: From \u2018blue fingers\u2019 to \u2018blue silver\u2019. A comparative overview of staining methods for in-gel proteomics","volume":"9","author":"Panfoli","year":"2012","journal-title":"Expert Rev. Proteom."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-8745-0_1","article-title":"Protein Stains and Applications","volume":"1853","author":"Sundaram","year":"2018","journal-title":"Protein Gel Detection and Imaging"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s11010-013-1627-5","article-title":"O-GlcNAcylation of \u03b1B-crystallin regulates its stress-induced translocation and cytoprotection","volume":"379","author":"Krishnamoorthy","year":"2013","journal-title":"Mol. Cell. Biochem."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/978-1-4939-8745-0_14","article-title":"Detection of Glycoproteins in Polyacrylamide Gels Using Pro-Q Emerald 300 Dye, a Fluorescent Periodate Schiff-Base Stain","volume":"1853","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_79","first-page":"33","article-title":"Phosphoproteomic analysis of aged skeletal muscle","volume":"22","author":"Gannon","year":"2008","journal-title":"Int. J. Mol. Med."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/978-1-4939-2550-6_23","article-title":"Principles and examples of gel-based approaches for phosphoprotein analysis","volume":"1295","author":"Steinberger","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/978-1-0716-2831-7_23","article-title":"Protein Digestion for 2D-DIGE Analysis","volume":"2596","author":"Murphy","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"5145","DOI":"10.1021\/pr300273g","article-title":"Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C\/trypsin proteolysis over trypsin digestion","volume":"11","author":"Glatter","year":"2012","journal-title":"J. Proteome Res."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1111\/febs.13287","article-title":"Proteomics beyond trypsin","volume":"282","author":"Tsiatsiani","year":"2015","journal-title":"FEBS J."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nprot.2016.057","article-title":"Six alternative proteases for mass spectrometry-based proteomics beyond trypsin","volume":"11","author":"Giansanti","year":"2016","journal-title":"Nat. Protoc."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"9523","DOI":"10.1021\/acs.analchem.0c00478","article-title":"Proteomics Using Protease Alternatives to Trypsin Benefits from Sequential Digestion with Trypsin","volume":"92","author":"Dau","year":"2020","journal-title":"Anal. Chem."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"S156","DOI":"10.1002\/elps.200900098","article-title":"Difference gel electrophoresis","volume":"30","author":"Minden","year":"2009","journal-title":"Electrophoresis"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1002\/prca.201400119","article-title":"State of the art of 2D DIGE","volume":"9","author":"Arentz","year":"2015","journal-title":"Proteom. Clin. Appl."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/978-1-4939-8793-1_20","article-title":"Two-Dimensional Difference Gel Electrophoresis","volume":"1855","author":"Blundon","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1007\/978-1-0716-2831-7_22","article-title":"Sample Preparation and Protein Determination for 2D-DIGE Proteomics","volume":"2596","author":"Gargan","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/978-1-0716-2831-7_2","article-title":"Top-Down Proteomics and Comparative 2D-DIGE Analysis","volume":"2596","author":"Ohlendieck","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1002\/1615-9861(200103)1:3<377::AID-PROT377>3.0.CO;2-6","article-title":"Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology","volume":"1","author":"Tonge","year":"2001","journal-title":"Proteomics"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1007\/s00216-005-3126-3","article-title":"The development of the DIGE system: 2D fluorescence difference gel analysis technology","volume":"382","author":"Marouga","year":"2005","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/978-1-0716-2831-7_11","article-title":"Comparative 3-Sample 2D-DIGE Analysis of Skeletal Muscles","volume":"2596","author":"Ohlendieck","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/978-1-0716-2831-7_3","article-title":"DIGE Analysis Software and Protein Identification Approaches","volume":"2596","author":"Dowling","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1007\/978-1-0716-2831-7_26","article-title":"Bioinformatic Analysis of the Subproteomic Profile of Cardiomyopathic Tissue","volume":"2596","author":"Murphy","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1002\/pmic.200401068","article-title":"Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens","volume":"5","author":"Nomura","year":"2005","journal-title":"Proteomics"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.pep.2012.09.007","article-title":"Affinity purification of protein complexes for analysis by multidimensional protein identification technology","volume":"86","author":"Banks","year":"2012","journal-title":"Protein Expr. Purif."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"4860","DOI":"10.1021\/pr900318k","article-title":"Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: Application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells","volume":"8","author":"Elschenbroich","year":"2009","journal-title":"J. Proteome Res."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1080\/14789450.2019.1575205","article-title":"Proteomic profiling of giant skeletal muscle proteins","volume":"16","author":"Murphy","year":"2019","journal-title":"Expert Rev. Proteom."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1002\/(SICI)1522-2683(20000101)21:2<446::AID-ELPS446>3.0.CO;2-9","article-title":"Agarose isoelectric focusing for the detection of many isoforms and high molecules in muscle protein analysis","volume":"21","author":"Hirabayashi","year":"2000","journal-title":"Electrophoresis"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.jchromb.2006.10.064","article-title":"Disease proteomics of high-molecular-mass proteins by two-dimensional gel electrophoresis with agarose gels in the first dimension (Agarose 2-DE)","volume":"849","author":"Maeda","year":"2007","journal-title":"J. Chromatogr. B Analyt. Technol. Biomed. Life Sci."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1002\/elps.202200255","article-title":"Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis","volume":"44","author":"Nakagawa","year":"2023","journal-title":"Electrophoresis"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Murphy, S., Henry, M., Meleady, P., and Ohlendieck, K. (2018). Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol. Methods Protoc., 3.","DOI":"10.1093\/biomethods\/bpy008"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"e93","DOI":"10.1002\/cpps.93","article-title":"Proteome Analysis Using Gel-LC-MS\/MS","volume":"96","author":"Goldman","year":"2019","journal-title":"Curr. Protoc. Protein Sci."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.ab.2017.11.022","article-title":"Proteomic profiling of large myofibrillar proteins from dried and long-term stored polyacrylamide gels","volume":"543","author":"Murphy","year":"2018","journal-title":"Anal. Biochem."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"e2222081120","DOI":"10.1073\/pnas.2222081120","article-title":"High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms","volume":"120","author":"Melby","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.jprot.2018.02.008","article-title":"Application of targeted mass spectrometry in bottom-up proteomics for systems biology research","volume":"189","author":"Manes","year":"2018","journal-title":"J. Proteom."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"5626","DOI":"10.1111\/febs.12502","article-title":"Proteomics methods for subcellular proteome analysis","volume":"280","author":"Drissi","year":"2013","journal-title":"FEBS J."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"3935","DOI":"10.1002\/pmic.201000289","article-title":"Subcellular fractionation methods and strategies for proteomics","volume":"10","author":"Lee","year":"2010","journal-title":"Proteomics"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-59745-281-6_5","article-title":"Organelle proteomics","volume":"519","author":"Granvogl","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41592-023-01791-5","article-title":"Single-cell proteomics enabled by next-generation sequencing or mass spectrometry","volume":"20","author":"Bennett","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_112","first-page":"239","article-title":"Fiber type diversity in skeletal muscle explored by mass spectrometry-based single fiber proteomics","volume":"35","author":"Schiaffino","year":"2020","journal-title":"Histol. Histopathol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"4060","DOI":"10.1021\/acs.jproteome.7b00433","article-title":"Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range","volume":"16","author":"Sielaff","year":"2017","journal-title":"J. Proteome Res."},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Duong, V.A., and Lee, H. (2023). Bottom-Up Proteomics: Advancements in Sample Preparation. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24065350"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth.1322","article-title":"Universal sample preparation method for proteome analysis","volume":"6","author":"Zougman","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1002\/pmic.201300553","article-title":"Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis","volume":"14","author":"Zougman","year":"2014","journal-title":"Proteomics"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"463352","DOI":"10.1016\/j.chroma.2022.463352","article-title":"Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications","volume":"1678","author":"Brandi","year":"2022","journal-title":"J. Chromatogr. A"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"e2200070","DOI":"10.1002\/pmic.202200070","article-title":"Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis","volume":"22","author":"Xie","year":"2022","journal-title":"Proteomics"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1002\/pmic.200600058","article-title":"Phosphoproteomics strategies for the functional analysis of signal transduction","volume":"6","author":"Morandell","year":"2006","journal-title":"Proteomics"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1007\/978-1-0716-2831-7_7","article-title":"DIGE-Based Phosphoproteomic Analysis","volume":"2596","author":"Stasyk","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"e2100216","DOI":"10.1002\/pmic.202100216","article-title":"Evaluation of four phosphopeptide enrichment strategies for mass spectrometry-based proteomic analysis","volume":"22","author":"Ino","year":"2022","journal-title":"Proteomics"},{"key":"ref_122","doi-asserted-by":"crossref","unstructured":"Sun, M., and Zhang, X. (2022). Current methodologies in protein ubiquitination characterization: From ubiquitinated protein to ubiquitin chain architecture. Cell Biosci., 12.","DOI":"10.1186\/s13578-022-00870-y"},{"key":"ref_123","doi-asserted-by":"crossref","unstructured":"Duong, V.A., Park, J.M., and Lee, H. (2020). Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21041524"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"100196","DOI":"10.1016\/j.xpro.2020.100196","article-title":"Protocol for the Bottom-Up Proteomic Analysis of Mouse Spleen","volume":"1","author":"Dowling","year":"2020","journal-title":"STAR Protoc."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1021\/acs.jproteome.9b00496","article-title":"LFQ-Analyst: An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant","volume":"19","author":"Shah","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1007\/978-1-0716-1024-4_23","article-title":"Label-Free Proteomics of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry","volume":"2228","author":"Distler","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"6889","DOI":"10.1007\/s00216-023-04759-8","article-title":"A review of the current state of single-cell proteomics and future perspective","volume":"415","author":"Ahmad","year":"2023","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1016\/j.gpb.2021.08.012","article-title":"Quantitative Proteomics Using Isobaric Labeling: A Practical Guide","volume":"19","author":"Chen","year":"2021","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"2913","DOI":"10.1021\/acs.jafc.6b05835","article-title":"Proteome Analysis Using Isobaric Tags for Relative and Absolute Analysis Quantitation (iTRAQ) Reveals Alterations in Stress-Induced Dysfunctional Chicken Muscle","volume":"65","author":"Xing","year":"2017","journal-title":"J. Agric. Food Chem."},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"e74","DOI":"10.1002\/cpps.74","article-title":"Quantitative Comparison of Proteomes Using SILAC","volume":"95","author":"Deng","year":"2019","journal-title":"Curr. Protoc. Protein Sci."},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"e2100256","DOI":"10.1002\/pmic.202100256","article-title":"Recent advances in isobaric labeling and applications in quantitative proteomics","volume":"22","author":"Sivanich","year":"2022","journal-title":"Proteomics"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"2028","DOI":"10.1002\/pmic.201600002","article-title":"Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells","volume":"16","author":"Lardenois","year":"2016","journal-title":"Proteomics"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1021\/acs.bioconjchem.1c00206","article-title":"Isotope-Coded Maleimide Affinity Tags for Proteomics Applications","volume":"32","author":"Wdowiak","year":"2021","journal-title":"Bioconjug. Chem."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1074\/mcp.M112.023127","article-title":"Identification of disease specific pathways using in vivo SILAC proteomics in dystrophin deficient mdx mouse","volume":"12","author":"Rayavarapu","year":"2013","journal-title":"Mol. Cell. Proteom."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"26504","DOI":"10.1021\/acsomega.0c03206","article-title":"Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys","volume":"5","author":"Alayi","year":"2020","journal-title":"ACS Omega"},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1002\/wdev.121","article-title":"Mass spectrometry-driven phosphoproteomics: Patterning the systems biology mosaic","volume":"3","author":"Aebersold","year":"2014","journal-title":"Wiley Interdiscip. Rev. Dev. Biol."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1074\/mcp.M110.000117","article-title":"Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria","volume":"10","author":"Deng","year":"2011","journal-title":"Mol. Cell. Proteom."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1002\/mas.21781","article-title":"Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape","volume":"42","author":"Kitata","year":"2023","journal-title":"Mass Spectrom. Rev."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.chroma.2017.10.043","article-title":"Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?","volume":"1526","author":"Fenaille","year":"2017","journal-title":"J. Chromatogr. A"},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Ludwig, C., Gillet, L., Rosenberger, G., Amon, S., Collins, B.C., and Aebersold, R. (2018). Data-independent acquisition-based SWATH-MS for quantitative proteomics: A tutorial. Mol. Syst. Biol., 14.","DOI":"10.15252\/msb.20178126"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"e2200179","DOI":"10.1002\/pmic.202200179","article-title":"Improving SWATH-MS analysis by deep-learning","volume":"23","author":"Sun","year":"2023","journal-title":"Proteomics"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"102712","DOI":"10.1016\/j.isci.2021.102712","article-title":"Skeletal muscle proteomes reveal downregulation of mitochondrial proteins in transition from prediabetes into type 2 diabetes","volume":"24","author":"Teppo","year":"2021","journal-title":"iScience"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1039\/C3AN01619F","article-title":"Protein microarray technology: How far off is routine diagnostics?","volume":"139","author":"Cretich","year":"2014","journal-title":"Analyst"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"918","DOI":"10.15252\/emmm.201303724","article-title":"Affinity proteomics within rare diseases: A BIO-NMD study for blood biomarkers of muscular dystrophies","volume":"6","author":"Ayoglu","year":"2014","journal-title":"EMBO Mol. Med."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Cosemans, G., Merckx, C., De Bleecker, J.L., and De Paepe, B. (2022). Inducible Heat Shock Protein 70 Levels in Patients and the mdx Mouse Affirm Regulation during Skeletal Muscle Regeneration in Muscular Dystrophy. Front. Biosci. (Schol. Ed.), 14.","DOI":"10.31083\/j.fbs1403019"},{"key":"ref_146","doi-asserted-by":"crossref","unstructured":"Aparna, G.M., and Tetala, K.K.R. (2023). Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules, 13.","DOI":"10.3390\/biom13040602"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1126\/science.1124619","article-title":"Mass spectrometry and protein analysis","volume":"312","author":"Domon","year":"2006","journal-title":"Science"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/pmic.200800441","article-title":"Proteomic profiling of antisense-induced exon skipping reveals reversal of pathobiochemical abnormalities in dystrophic mdx diaphragm","volume":"9","author":"Doran","year":"2009","journal-title":"Proteomics"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/978-1-61779-418-6_10","article-title":"Proteomic analysis of skeletal muscle tissue using SELDI-TOF MS: Application to disuse atrophy","volume":"818","author":"Clarke","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"3241","DOI":"10.1002\/1522-2683(200209)23:18<3241::AID-ELPS3241>3.0.CO;2-D","article-title":"Application of surface-enhanced laser desorption\/ionization technology to the detection and identification of urinary parvalbumin-alpha: A biomarker of compound-induced skeletal muscle toxicity in the rat","volume":"23","author":"Dare","year":"2002","journal-title":"Electrophoresis"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/nmeth1088","article-title":"Analysis and validation of proteomic data generated by tandem mass spectrometry","volume":"4","author":"Nesvizhskii","year":"2007","journal-title":"Nat. Methods"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1146\/annurev-bioeng-061008-124934","article-title":"Proteomics by mass spectrometry: Approaches, advances, and applications","volume":"11","author":"Yates","year":"2009","journal-title":"Annu. Rev. Biomed. Eng."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"e4612","DOI":"10.1002\/pro.4612","article-title":"Dissecting the structural heterogeneity of proteins by native mass spectrometry","volume":"32","author":"Reid","year":"2023","journal-title":"Protein Sci."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41570-021-00353-7","article-title":"Studying protein structure and function by native separation-mass spectrometry","volume":"6","author":"Haselberg","year":"2022","journal-title":"Nat. Rev. Chem."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1042\/EBC20220191","article-title":"Surface-sampling mass spectrometry to study proteins and protein complexes","volume":"67","author":"Wong","year":"2023","journal-title":"Essays Biochem."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1477-5956-12-25","article-title":"Proteomic analysis of laser capture microscopy purified myotendinous junction regions from muscle sections","volume":"12","author":"Can","year":"2014","journal-title":"Proteome Sci."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"C381","DOI":"10.1152\/ajpcell.00317.2015","article-title":"Myosin content of individual human muscle fibers isolated by laser capture microdissection","volume":"310","author":"Stuart","year":"2016","journal-title":"Am. J. Physiol. Cell Physiol."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.jgg.2023.07.011","article-title":"Laser capture microdissection for biomedical research: Towards high-throughput, multi-omics, and single-cell resolution","volume":"50","author":"Guo","year":"2023","journal-title":"J. Genet. Genom."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"pgac086","DOI":"10.1093\/pnasnexus\/pgac086","article-title":"Signatures of muscle disuse in spaceflight and bed rest revealed by single muscle fiber proteomics","volume":"1","author":"Murgia","year":"2022","journal-title":"PNAS Nexus"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1002\/prca.201400130","article-title":"ELISA in the multiplex era: Potentials and pitfalls","volume":"9","author":"Tighe","year":"2015","journal-title":"Proteom. Clin. Appl."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/978-1-0716-2376-3_10","article-title":"Enzyme-Linked Immunosorbent Assay (ELISA)","volume":"2508","author":"Tabatabaei","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1007\/978-1-0716-2772-3_18","article-title":"Assessment of the Gene Therapy Immune Response in the Canine Muscular Dystrophy Model","volume":"2587","author":"Hakim","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/978-1-0716-2831-7_29","article-title":"Immunoblot Analysis of DIGE-Based Proteomics","volume":"2596","author":"Landsberger","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1080\/14789450.2017.1388167","article-title":"Protein purification and analysis: Next generation Western blotting techniques","volume":"14","author":"Mishra","year":"2017","journal-title":"Expert Rev. Proteom."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/978-1-62703-556-9_17","article-title":"Gel electrophoresis-based proteomics of senescent tissues","volume":"1048","author":"Carberry","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1208\/s12248-014-9660-1","article-title":"Next generation ligand binding assays-review of emerging technologies\u2019 capabilities to enhance throughput and multiplexing","volume":"16","author":"Mora","year":"2014","journal-title":"AAPS J."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.4155\/bio-2019-0163","article-title":"Establishment of neurofilament light chain Simoa assay in cerebrospinal fluid and blood","volume":"11","author":"Hendricks","year":"2019","journal-title":"Bioanalysis"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1038\/s41374-022-00830-7","article-title":"High-throughput proteomics: A methodological mini-review","volume":"102","author":"Cui","year":"2022","journal-title":"Lab. Invest."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/978-1-0716-2831-7_31","article-title":"Histological and Histochemical Microscopy Used to Verify 2D-DIGE Pathoproteomics","volume":"2596","author":"Zweyer","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1007\/978-1-0716-2831-7_30","article-title":"Verification of Protein Changes Determined by 2D-DIGE Based Proteomics Using Immunofluorescence Microscopy","volume":"2596","author":"Zweyer","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_171","first-page":"493","article-title":"History and development of staining methods for skeletal muscle fiber types","volume":"37","author":"Sawano","year":"2022","journal-title":"Histol. Histopathol."},{"key":"ref_172","first-page":"101","article-title":"Histopathology of Duchenne muscular dystrophy in correlation with changes in proteomic biomarkers","volume":"37","author":"Zweyer","year":"2022","journal-title":"Histol. Histopathol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"15336","DOI":"10.1038\/s41598-020-70885-3","article-title":"Decoding mitochondrial heterogeneity in single muscle fibres by imaging mass cytometry","volume":"10","author":"Warren","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1002\/cyto.a.24535","article-title":"TITAN: An end-to-end data analysis environment for the Hyperion\u2122 imaging system","volume":"101","author":"Thirumal","year":"2022","journal-title":"Cytometry A"},{"key":"ref_175","doi-asserted-by":"crossref","unstructured":"Park, J., Kim, J., Lewy, T., Rice, C.M., Elemento, O., Rendeiro, A.F., and Mason, C.E. (2022). Spatial omics technologies at multimodal and single cell\/subcellular level. Genome Biol., 23.","DOI":"10.1186\/s13059-022-02824-6"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"181","DOI":"10.4155\/bio-2020-0267","article-title":"Flow cytometry: Principles, applications and recent advances","volume":"13","author":"Manohar","year":"2021","journal-title":"Bioanalysis"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"dev174177","DOI":"10.1242\/dev.174177","article-title":"Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions","volume":"146","author":"Juan","year":"2019","journal-title":"Development"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"S325","DOI":"10.3233\/JND-210706","article-title":"The Effect of Immunomodulatory Treatments on Anti-Dystrophin Immune Response After AAV Gene Therapy in Dystrophin Deficient mdx Mice","volume":"8","author":"Li","year":"2021","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"946","DOI":"10.2174\/1389203717666160724202806","article-title":"Chemical Crosslinking: Role in Protein and Peptide Science","volume":"18","author":"Arora","year":"2017","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"17","DOI":"10.12688\/hrbopenres.12846.1","article-title":"Chemical crosslinking analysis of \u03b2-dystroglycan in dystrophin-deficient skeletal muscle","volume":"1","author":"Murphy","year":"2018","journal-title":"HRB Open Res."},{"key":"ref_181","doi-asserted-by":"crossref","unstructured":"Jayachandran, B., Parvin, T.N., Alam, M.M., Chanda, K., and Mm, B. (2022). Insights on Chemical Crosslinking Strategies for Proteins. Molecules, 27.","DOI":"10.3390\/molecules27238124"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1007\/978-1-0716-2831-7_27","article-title":"Elucidating Cellular Metabolism and Protein Difference Data from DIGE Proteomics Experiments Using Enzyme Assays","volume":"2596","author":"Dowd","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"5509","DOI":"10.1002\/pmic.200900472","article-title":"Proteomic DIGE analysis of the mitochondria-enriched fraction from aged rat skeletal muscle","volume":"9","author":"Ohlendieck","year":"2009","journal-title":"Proteomics"},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/978-1-0716-2831-7_28","article-title":"Enzyme Assay Methods to Validate DIGE Proteomics Data","volume":"2596","author":"Dowd","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/2044-5040-1-6","article-title":"Skeletal muscle proteomics: Current approaches, technical challenges and emerging techniques","volume":"1","author":"Ohlendieck","year":"2011","journal-title":"Skelet. Muscle"},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13395-018-0152-3","article-title":"Diversification of the muscle proteome through alternative splicing","volume":"8","author":"Nakka","year":"2018","journal-title":"Skelet. Muscle"},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/s00223-014-9915-y","article-title":"Skeletal muscle: A brief review of structure and function","volume":"96","author":"Frontera","year":"2015","journal-title":"Calcif. Tissue Int."},{"key":"ref_188","doi-asserted-by":"crossref","unstructured":"Mukund, K., and Subramaniam, S. (2020). Skeletal muscle: A review of molecular structure and function, in health and disease. Wiley Interdiscip. Rev. Syst. Biol. Med., 12.","DOI":"10.1002\/wsbm.1462"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/B978-0-323-98818-6.00013-3","article-title":"Skeletal muscle structure, physiology, and function","volume":"195","author":"Brooks","year":"2023","journal-title":"Handb. Clin. Neurol."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1152\/physrev.00031.2010","article-title":"Fiber types in mammalian skeletal muscles","volume":"91","author":"Schiaffino","year":"2011","journal-title":"Physiol. Rev."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1111\/j.1748-1716.2010.02130.x","article-title":"Fibre types in skeletal muscle: A personal account","volume":"199","author":"Schiaffino","year":"2010","journal-title":"Acta Physiol."},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0079-6107(00)00006-7","article-title":"Human skeletal muscle fibres: Molecular and functional diversity","volume":"73","author":"Bottinelli","year":"2000","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"C409","DOI":"10.1152\/ajpcell.00212.2021","article-title":"Murine models of Duchenne muscular dystrophy: Is there a best model?","volume":"321","author":"Swiderski","year":"2021","journal-title":"Am. J. Physiol. Cell Physiol."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0012-1606(88)90183-2","article-title":"Embryonic and neonatal myosin heavy chain in denervated and paralyzed rat skeletal muscle","volume":"127","author":"Schiaffino","year":"1988","journal-title":"Dev. Biol."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"dev184507","DOI":"10.1242\/dev.184507","article-title":"Myosin heavy chain-embryonic regulates skeletal muscle differentiation during mammalian development","volume":"147","author":"Agarwal","year":"2020","journal-title":"Development"},{"key":"ref_196","doi-asserted-by":"crossref","unstructured":"Gargan, S., Dowling, P., Zweyer, M., Reimann, J., Henry, M., Meleady, P., Swandulla, D., and Ohlendieck, K. (2021). Mass Spectrometric Profiling of Extraocular Muscle and Proteomic Adaptations in the mdx-4cv Model of Duchenne Muscular Dystrophy. Life, 11.","DOI":"10.3390\/life11070595"},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s00360-023-01499-0","article-title":"Developmental, physiologic and phylogenetic perspectives on the expression and regulation of myosin heavy chains in mammalian skeletal muscles","volume":"193","author":"Hoh","year":"2023","journal-title":"J. Comp. Physiol. B"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s004180100268","article-title":"Transitions of muscle fiber phenotypic profiles","volume":"115","author":"Pette","year":"2001","journal-title":"Histochem. Cell Biol."},{"key":"ref_199","first-page":"119","article-title":"Proteomic profiling of skeletal muscle plasticity","volume":"1","author":"Ohlendieck","year":"2012","journal-title":"Muscles Ligaments Tendons J."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1113\/JP275443","article-title":"The impact of exercise and nutrition on the regulation of skeletal muscle mass","volume":"597","author":"McGlory","year":"2019","journal-title":"J. Physiol."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1152\/japplphysiol.00624.2019","article-title":"Fiber typing human skeletal muscle with fluorescent immunohistochemistry","volume":"127","author":"Murach","year":"2019","journal-title":"J. Appl. Physiol."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13395-020-00226-5","article-title":"High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers","volume":"10","author":"Kallabis","year":"2020","journal-title":"Skelet. Muscle"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1021\/jasms.3c00072","article-title":"A Complete Workflow for High Throughput Human Single Skeletal Muscle Fiber Proteomics","volume":"34","author":"Momenzadeh","year":"2023","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1369\/0022155411426780","article-title":"The skeletal muscle satellite cell: Still young and fascinating at 50","volume":"59","year":"2011","journal-title":"J. Histochem. Cytochem."},{"key":"ref_205","doi-asserted-by":"crossref","unstructured":"Negroni, E., Kondili, M., Muraine, L., Bensalah, M., Butler-Browne, G.S., Mouly, V., Bigot, A., and Trollet, C. (2022). Muscle fibro-adipogenic progenitors from a single-cell perspective: Focus on their \u201cvirtual\u201d secretome. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.952041"},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"e15480","DOI":"10.14814\/phy2.15480","article-title":"Role of macrophages during skeletal muscle regeneration and hypertrophy-Implications for immunomodulatory strategies","volume":"10","author":"Bernard","year":"2022","journal-title":"Physiol. Rep."},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"S183","DOI":"10.3233\/JND-210705","article-title":"The Satellite Cell at 60: The Foundation Years","volume":"8","author":"Engquist","year":"2021","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1016\/S1357-2725(03)00042-6","article-title":"Muscle satellite cells","volume":"35","author":"Morgan","year":"2003","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_209","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.semcdb.2015.09.017","article-title":"PAX3 and PAX7 as upstream regulators of myogenesis","volume":"44","author":"Buckingham","year":"2015","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.semcdb.2017.11.011","article-title":"Function of the myogenic regulatory factors Myf5, MyoD, Myogenin and MRF4 in skeletal muscle, satellite cells and regenerative myogenesis","volume":"72","author":"Zammit","year":"2017","journal-title":"Semin. Cell Dev. Biol."},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1083\/jcb.151.6.1221","article-title":"Expression of CD34 and Myf5 defines the majority of quiescent adult skeletal muscle satellite cells","volume":"151","author":"Beauchamp","year":"2000","journal-title":"J. Cell Biol."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/978-3-031-07167-6_10","article-title":"The Cellular Basis for the Generation of Firing Patterns in Human Motor Units","volume":"28","author":"Khurram","year":"2022","journal-title":"Adv. Neurobiol."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1007\/978-1-0716-2831-7_20","article-title":"Identification of Subproteomic Markers for Skeletal Muscle Profiling","volume":"2596","author":"Dowling","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1210\/endrev\/bnaa016","article-title":"Muscle-Organ Crosstalk: The Emerging Roles of Myokines","volume":"41","author":"Severinsen","year":"2020","journal-title":"Endocr. Rev."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1007\/s11914-020-00599-y","article-title":"Muscle, Bone, and Fat Crosstalk: The Biological Role of Myokines, Osteokines, and Adipokines","volume":"18","author":"Kirk","year":"2020","journal-title":"Curr. Osteoporos. Rep."},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1007\/s11914-020-00602-6","article-title":"Bone-Muscle Mutual Interactions","volume":"18","author":"Johnson","year":"2020","journal-title":"Curr. Osteoporos. Rep."},{"key":"ref_217","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/bs.acc.2019.07.010","article-title":"Myokines: The endocrine coupling of skeletal muscle and bone","volume":"94","author":"Gomarasca","year":"2020","journal-title":"Adv. Clin. Chem."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"100019","DOI":"10.1016\/j.ocarto.2019.100019","article-title":"The secretome of skeletal muscle cells: A systematic review","volume":"2","author":"Florin","year":"2020","journal-title":"Osteoarthr. Cartil. Open."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.jprot.2012.09.008","article-title":"In-depth analysis of the secretome identifies three major independent secretory pathways in differentiating human myoblasts","volume":"77","author":"Bigot","year":"2012","journal-title":"J. Proteom."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1016\/j.bbapap.2013.08.004","article-title":"Secretome profiling of primary human skeletal muscle cells","volume":"1844","author":"Hartwig","year":"2014","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_221","doi-asserted-by":"crossref","first-page":"709807","DOI":"10.3389\/fphys.2021.709807","article-title":"The Role of the Skeletal Muscle Secretome in Mediating Endurance and Resistance Training Adaptations","volume":"12","author":"Leuchtmann","year":"2021","journal-title":"Front. Physiol."},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.medcli.2021.09.025","article-title":"Rhabdomyolysis: A syndrome to be considered. Rabdomi\u00f3lisis: Un s\u00edndrome a tener en cuenta","volume":"158","year":"2022","journal-title":"Med. Clin."},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1097\/WCO.0000000000001096","article-title":"Recent advances in our understanding of genetic rhabdomyolysis","volume":"35","author":"Ravenscroft","year":"2022","journal-title":"Curr. Opin. Neurol."},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"101015","DOI":"10.1016\/j.disamonth.2020.101015","article-title":"Rhabdomyolysis","volume":"66","author":"Cabral","year":"2020","journal-title":"Dis. Mon."},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"104498","DOI":"10.1016\/j.jprot.2022.104498","article-title":"Urine proteomics as a non-invasive approach to monitor exertional rhabdomyolysis during military training","volume":"258","author":"Carneiro","year":"2022","journal-title":"J. Proteom."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1074\/mcp.M114.044222","article-title":"Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors","volume":"14","author":"Deshmukh","year":"2015","journal-title":"Mol. Cell. Proteom."},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1074\/mcp.M700304-MCP200","article-title":"Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS\/MS","volume":"7","author":"Yi","year":"2008","journal-title":"Mol. Cell. Proteom."},{"key":"ref_228","doi-asserted-by":"crossref","first-page":"3265","DOI":"10.1021\/pr800873q","article-title":"Characterization of human skeletal muscle biopsy samples using shotgun proteomics","volume":"8","author":"Parker","year":"2009","journal-title":"J. Proteome Res."},{"key":"ref_229","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1002\/pmic.200700902","article-title":"A proteome map of murine heart and skeletal muscle","volume":"8","author":"Raddatz","year":"2008","journal-title":"Proteomics"},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1002\/pmic.201400118","article-title":"Label-free profiling of skeletal muscle using high-definition mass spectrometry","volume":"14","author":"Burniston","year":"2014","journal-title":"Proteomics"},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"290","DOI":"10.3390\/proteomes1030290","article-title":"Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity","volume":"1","author":"Malik","year":"2013","journal-title":"Proteomes"},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/s10974-019-09507-z","article-title":"Proteomic profiling of the mouse diaphragm and refined mass spectrometric analysis of the dystrophic phenotype","volume":"40","author":"Murphy","year":"2019","journal-title":"J. Muscle Res. Cell Motil."},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/pmic.200401183","article-title":"Comparison of protein expression in human deltoideus and vastus lateralis muscles using two-dimensional gel electrophoresis","volume":"5","author":"Capitanio","year":"2005","journal-title":"Proteomics"},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"M111.010801","DOI":"10.1074\/mcp.M111.010801","article-title":"On marathons and Sprints: An integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers","volume":"11","author":"Drexler","year":"2012","journal-title":"Mol. Cell. Proteom."},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1002\/pmic.200501337","article-title":"2-D protein maps of rat gastrocnemius and soleus muscles: A tool for muscle plasticity assessment","volume":"6","author":"Gelfi","year":"2006","journal-title":"Proteomics"},{"key":"ref_236","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1002\/pmic.200401181","article-title":"Proteomic analysis of slow- and fast-twitch skeletal muscles","volume":"5","author":"Okumura","year":"2005","journal-title":"Proteomics"},{"key":"ref_237","doi-asserted-by":"crossref","unstructured":"Eggers, B., Schork, K., Turewicz, M., Barkovits, K., Eisenacher, M., Schr\u00f6der, R., Clemen, C.S., and Marcus, K. (2021). Advanced fiber type- specific protein profiles derived from adult murine skeletal muscle. Proteomes, 9.","DOI":"10.3390\/proteomes9020028"},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"2396","DOI":"10.1016\/j.celrep.2017.05.054","article-title":"Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging","volume":"19","author":"Murgia","year":"2017","journal-title":"Cell Rep."},{"key":"ref_239","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13395-021-00279-0","article-title":"Protein profile of fiber types in human skeletal muscle: A single-fiber proteomics study","volume":"11","author":"Murgia","year":"2021","journal-title":"Skelet. Muscle"},{"key":"ref_240","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1038\/s41467-020-20556-8","article-title":"Deep muscle-proteomic analysis of freeze-dried human muscle biopsies reveals fiber type-specific adaptations to exercise training","volume":"12","author":"Deshmukh","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_241","doi-asserted-by":"crossref","unstructured":"Hadr\u00e9vi, J., Hellstr\u00f6m, F., Kieselbach, T., Malm, C., and Pedrosa-Domell\u00f6f, F. (2011). Protein differences between human trapezius and vastus lateralis muscles determined with a proteomic approach. BMC Musculoskelet. Disord., 12.","DOI":"10.1186\/1471-2474-12-181"},{"key":"ref_242","doi-asserted-by":"crossref","unstructured":"Tan, X., He, Y., He, Y., Yan, Z., Chen, J., Zhao, R., Sui, X., Zhang, L., Du, X., and Irwin, D.M. (2023). Comparative Proteomic Analysis of Glycolytic and Oxidative Muscle in Pigs. Genes, 14.","DOI":"10.3390\/genes14020361"},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1097\/WCO.0000000000001191","article-title":"An update on Becker muscular dystrophy","volume":"36","author":"Straub","year":"2023","journal-title":"Curr. Opin. Neurol."},{"key":"ref_244","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1002\/humu.21114","article-title":"Mutational spectrum of DMD mutations in dystrophinopathy patients: Application of modern diagnostic techniques to a large cohort","volume":"30","author":"Flanigan","year":"2009","journal-title":"Hum. Mutat."},{"key":"ref_245","doi-asserted-by":"crossref","unstructured":"Juan-Mateu, J., Gonzalez-Quereda, L., Rodriguez, M.J., Baena, M., Verdura, E., Nascimento, A., Ortez, C., Baiget, M., and Gallano, P. (2015). DMD Mutations in 576 Dystrophinopathy Families: A Step Forward in Genotype-Phenotype Correlations. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0135189"},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/humu.22758","article-title":"The TREAT-NMD DMD Global Database: Analysis of more than 7000 Duchenne muscular dystrophy mutations","volume":"36","author":"Bladen","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_247","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/S1474-4422(03)00585-4","article-title":"Dystrophin and mutations: One gene, several proteins, multiple phenotypes","volume":"2","author":"Muntoni","year":"2003","journal-title":"Lancet Neurol."},{"key":"ref_248","first-page":"1","article-title":"Towards an understanding of the dystrophin-glycoprotein complex: Linkage between the extracellular matrix and the membrane cytoskeleton in muscle fibers","volume":"69","author":"Ohlendieck","year":"1996","journal-title":"Eur. J. Cell Biol."},{"key":"ref_249","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/345315a0","article-title":"Deficiency of a glycoprotein component of the dystrophin complex in dystrophic muscle","volume":"345","author":"Ervasti","year":"1990","journal-title":"Nature"},{"key":"ref_250","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1083\/jcb.115.6.1685","article-title":"Dystrophin-associated proteins are greatly reduced in skeletal muscle from mdx mice","volume":"115","author":"Ohlendieck","year":"1991","journal-title":"J. Cell Biol."},{"key":"ref_251","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1212\/WNL.43.4.795","article-title":"Duchenne muscular dystrophy: Deficiency of dystrophin-associated proteins in the sarcolemma","volume":"43","author":"Ohlendieck","year":"1993","journal-title":"Neurology"},{"key":"ref_252","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1083\/jcb.122.4.809","article-title":"A role for the dystrophin-glycoprotein complex as a transmembrane linker between laminin and actin","volume":"122","author":"Ervasti","year":"1993","journal-title":"J. Cell Biol."},{"key":"ref_253","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.csbj.2015.11.002","article-title":"The biochemical and mass spectrometric profiling of the dystrophin complexome from skeletal muscle","volume":"14","author":"Murphy","year":"2015","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_254","doi-asserted-by":"crossref","unstructured":"Dowling, P., Gargan, S., Murphy, S., Zweyer, M., Sabir, H., Swandulla, D., and Ohlendieck, K. (2021). The Dystrophin Node as Integrator of Cytoskeletal Organization, Lateral Force Transmission, Fiber Stability and Cellular Signaling in Skeletal Muscle. Proteomes, 9.","DOI":"10.3390\/proteomes9010009"},{"key":"ref_255","doi-asserted-by":"crossref","unstructured":"Zab\u0142ocka, B., G\u00f3recki, D.C., and Zab\u0142ocki, K. (2021). Disrupted Calcium Homeostasis in Duchenne Muscular Dystrophy: A Common Mechanism behind Diverse Consequences. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222011040"},{"key":"ref_256","doi-asserted-by":"crossref","first-page":"e2200003","DOI":"10.1002\/pmic.202200003","article-title":"Proteomic profiling of impaired excitation-contraction coupling and abnormal calcium handling in muscular dystrophy","volume":"22","author":"Dowling","year":"2022","journal-title":"Proteomics"},{"key":"ref_257","doi-asserted-by":"crossref","unstructured":"Dubinin, M.V., and Belosludtsev, K.N. (2023). Ion Channels of the Sarcolemma and Intracellular Organelles in Duchenne Muscular Dystrophy: A Role in the Dysregulation of Ion Homeostasis and a Possible Target for Therapy. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24032229"},{"key":"ref_258","first-page":"11856","article-title":"Cellular pathogenesis of Duchenne muscular dystrophy: Progressive myofibre degeneration, chronic inflammation, reactive myofibrosis and satellite cell dysfunction","volume":"33","author":"Dowling","year":"2023","journal-title":"Eur. J. Transl. Myol."},{"key":"ref_259","doi-asserted-by":"crossref","unstructured":"Dowling, P., Gargan, S., Zweyer, M., Swandulla, D., and Ohlendieck, K. (2023). Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules, 13.","DOI":"10.3390\/biom13071108"},{"key":"ref_260","doi-asserted-by":"crossref","first-page":"680","DOI":"10.2174\/13892037113146660083","article-title":"Proteomics of the dystrophin-glycoprotein complex and dystrophinopathy","volume":"14","author":"Holland","year":"2013","journal-title":"Curr. Protein Pept. Sci."},{"key":"ref_261","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1080\/14789450.2016.1202768","article-title":"Understanding the molecular consequences of inherited muscular dystrophies: Advancements through proteomic experimentation","volume":"13","author":"Fuller","year":"2016","journal-title":"Expert Rev. Proteom."},{"key":"ref_262","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1002\/pmic.201500158","article-title":"Pathoproteomic profiling of the skeletal muscle matrisome in dystrophinopathy associated myofibrosis","volume":"16","author":"Holland","year":"2016","journal-title":"Proteomics"},{"key":"ref_263","doi-asserted-by":"crossref","first-page":"1700071","DOI":"10.1002\/prca.201700071","article-title":"Mass spectrometry-based protein analysis to unravel the tissue pathophysiology in Duchenne muscular dystrophy","volume":"12","author":"Carr","year":"2018","journal-title":"Proteom. Clin. Appl."},{"key":"ref_264","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1080\/14737159.2019.1648214","article-title":"Emerging proteomic biomarkers of X-linked muscular dystrophy","volume":"19","author":"Dowling","year":"2019","journal-title":"Expert Rev. Mol. Diagn."},{"key":"ref_265","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1080\/14789450.2020.1773806","article-title":"Duchenne muscular dystrophy: Recent advances in protein biomarkers and the clinical application","volume":"17","year":"2020","journal-title":"Expert Rev. Proteom."},{"key":"ref_266","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1002\/pmic.200300561","article-title":"Proteomic analysis of mdx skeletal muscle: Great reduction of adenylate kinase 1 expression and enzymatic activity","volume":"3","author":"Ge","year":"2003","journal-title":"Proteomics"},{"key":"ref_267","doi-asserted-by":"crossref","first-page":"4610","DOI":"10.1002\/pmic.200600082","article-title":"Proteome analysis of the dystrophin-deficient MDX diaphragm reveals a drastic increase in the heat shock protein cvHSP","volume":"6","author":"Doran","year":"2006","journal-title":"Proteomics"},{"key":"ref_268","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.bbapap.2006.01.007","article-title":"Reduced expression of regucalcin in young and aged mdx diaphragm indicates abnormal cytosolic calcium handling in dystrophin-deficient muscle","volume":"1764","author":"Doran","year":"2006","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_269","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3892\/ijmm.2012.1006","article-title":"Proteomics reveals drastic increase of extracellular matrix proteins collagen and dermatopontin in the aged mdx diaphragm model of Duchenne muscular dystrophy","volume":"30","author":"Carberry","year":"2012","journal-title":"Int. J. Mol. Med."},{"key":"ref_270","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1007\/s00421-011-1906-3","article-title":"Proteomic assessment of the acute phase of dystrophin deficiency in mdx mice","volume":"111","author":"Dixon","year":"2011","journal-title":"Eur. J. Appl. Physiol."},{"key":"ref_271","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1021\/pr2001385","article-title":"Quantitative proteomic analysis of dystrophic dog muscle","volume":"10","author":"Guevel","year":"2011","journal-title":"J. Proteome Res."},{"key":"ref_272","doi-asserted-by":"crossref","first-page":"4413","DOI":"10.1021\/pr300328r","article-title":"Comparative proteomic profiling of dystroglycan-associated proteins in wild type, mdx, and Galgt2 transgenic mouse skeletal muscle","volume":"11","author":"Yoon","year":"2012","journal-title":"J. Proteome Res."},{"key":"ref_273","doi-asserted-by":"crossref","first-page":"2576","DOI":"10.1002\/elps.200406013","article-title":"Differential expression of the skeletal muscle proteome in mdx mice at different ages","volume":"25","author":"Ge","year":"2004","journal-title":"Electrophoresis"},{"key":"ref_274","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.3390\/biology2041438","article-title":"Application of fluorescence two-dimensional difference in-gel electrophoresis as a proteomic biomarker discovery tool in muscular dystrophy research","volume":"2","author":"Carberry","year":"2013","journal-title":"Biology"},{"key":"ref_275","doi-asserted-by":"crossref","unstructured":"Matsumura, C.Y., Menezes de Oliveira, B., Durbeej, M., and Marques, M.J. (2013). Isobaric Tagging-Based Quantification for Proteomic Analysis: A Comparative Study of Spared and Affected Muscles from mdx Mice at the Early Phase of Dystrophy. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0065831"},{"key":"ref_276","doi-asserted-by":"crossref","first-page":"2318","DOI":"10.1002\/pmic.201400471","article-title":"Label-free mass spectrometric analysis of the mdx-4cv diaphragm identifies the matricellular protein periostin as a potential factor involved in dystrophinopathy-related fibrosis","volume":"15","author":"Holland","year":"2015","journal-title":"Proteomics"},{"key":"ref_277","doi-asserted-by":"crossref","first-page":"6756","DOI":"10.1093\/hmg\/ddv381","article-title":"Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration","volume":"24","author":"Roberts","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"ref_278","doi-asserted-by":"crossref","first-page":"11317","DOI":"10.3390\/molecules200611317","article-title":"Comparative Label-Free Mass Spectrometric Analysis of Mildly versus Severely Affected mdx Mouse Skeletal Muscles Identifies Annexin, Lamin, and Vimentin as Universal Dystrophic Markers","volume":"20","author":"Holland","year":"2015","journal-title":"Molecules"},{"key":"ref_279","doi-asserted-by":"crossref","first-page":"397","DOI":"10.3390\/biology4020397","article-title":"Simultaneous Pathoproteomic Evaluation of the Dystrophin-Glycoprotein Complex and Secondary Changes in the mdx-4cv Mouse Model of Duchenne Muscular Dystrophy","volume":"4","author":"Murphy","year":"2015","journal-title":"Biology"},{"key":"ref_280","doi-asserted-by":"crossref","first-page":"33362","DOI":"10.1038\/srep33362","article-title":"Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy","volume":"6","author":"Kemter","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_281","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1074\/mcp.M116.059188","article-title":"Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy","volume":"15","author":"Turk","year":"2016","journal-title":"Mol. Cell. Proteom."},{"key":"ref_282","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/s10974-017-9478-4","article-title":"Proteomic profiling of the dystrophin complex and membrane fraction from dystrophic mdx muscle reveals decreases in the cytolinker desmoglein and increases in the extracellular matrix stabilizers biglycan and fibronectin","volume":"38","author":"Murphy","year":"2017","journal-title":"J. Muscle Res. Cell Motil."},{"key":"ref_283","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.jprot.2017.09.009","article-title":"Proteome analysis in dystrophic mdx mouse muscle reveals a drastic alteration of key metabolic and contractile proteins after chronic exercise and the potential modulation by anti-oxidant compounds","volume":"170","author":"Gamberi","year":"2018","journal-title":"J. Proteom."},{"key":"ref_284","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1002\/elps.201800028","article-title":"Comparative gel-based proteomic analysis of chemically crosslinked complexes in dystrophic skeletal muscle","volume":"39","author":"Murphy","year":"2018","journal-title":"Electrophoresis"},{"key":"ref_285","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.jprot.2018.01.015","article-title":"Proteomic analysis of the sarcolemma-enriched fraction from dystrophic mdx-4cv skeletal muscle","volume":"191","author":"Murphy","year":"2019","journal-title":"J. Proteom."},{"key":"ref_286","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1002\/jcsm.12527","article-title":"Comparative proteomic analyses of Duchenne muscular dystrophy and Becker muscular dystrophy muscles: Changes contributing to preserve muscle function in Becker muscular dystrophy patients","volume":"11","author":"Capitanio","year":"2020","journal-title":"J. Cachexia Sarcopenia Muscle"},{"key":"ref_287","doi-asserted-by":"crossref","unstructured":"Capitanio, D., Moriggi, M., Barbacini, P., Torretta, E., Moroni, I., Blasevich, F., Morandi, L., Mora, M., and Gelfi, C. (2020). Molecular fingerprint of BMD patients lacking a portion in the rod domain of dystrophin. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23052624"},{"key":"ref_288","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1074\/mcp.RA120.002345","article-title":"Mutation-independent proteomic signatures of pathological progression in murine models of Duchenne muscular dystrophy","volume":"19","author":"Johansson","year":"2020","journal-title":"Mol. Cell. Proteom."},{"key":"ref_289","doi-asserted-by":"crossref","first-page":"dmm049285","DOI":"10.1242\/dmm.049285","article-title":"A scalable, clinically severe pig model for Duchenne muscular dystrophy","volume":"14","author":"Stirm","year":"2021","journal-title":"Dis. Models Mech."},{"key":"ref_290","doi-asserted-by":"crossref","unstructured":"Gargan, S., Dowling, P., Zweyer, M., Henry, M., Meleady, P., Swandulla, D., and Ohlendieck, K. (2022). Proteomic Identification of Markers of Membrane Repair, Regeneration and Fibrosis in the Aged and Dystrophic Diaphragm. Life, 12.","DOI":"10.3390\/life12111679"},{"key":"ref_291","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.freeradbiomed.2022.10.300","article-title":"A deep redox proteome profiling workflow and its application to skeletal muscle of a Duchenne Muscular Dystrophy model","volume":"193","author":"Day","year":"2022","journal-title":"Free Radic. Biol. Med."},{"key":"ref_292","doi-asserted-by":"crossref","unstructured":"Mucha, O., Myszka, M., Podkalicka, P., \u015awiderska, B., Malinowska, A., Dulak, J., and \u0141oboda, A. (2023). Proteome Profiling of the Dystrophic mdx Mice Diaphragm. Biomolecules, 13.","DOI":"10.3390\/biom13111648"},{"key":"ref_293","doi-asserted-by":"crossref","unstructured":"Ng, S.Y., and Ljubicic, V. (2020). Recent insights into neuromuscular junction biology in Duchenne muscular dystrophy: Impacts, challenges, and opportunities. EBioMedicine, 61.","DOI":"10.1016\/j.ebiom.2020.103032"},{"key":"ref_294","doi-asserted-by":"crossref","unstructured":"Meyers, T.A., and Townsend, D. (2019). Cardiac Pathophysiology and the Future of Cardiac Therapies in Duchenne Muscular Dystrophy. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20174098"},{"key":"ref_295","doi-asserted-by":"crossref","first-page":"5447","DOI":"10.1007\/s00018-021-03862-2","article-title":"The multifaceted view of heart problem in Duchenne muscular dystrophy","volume":"78","author":"Polak","year":"2021","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_296","doi-asserted-by":"crossref","first-page":"00176","DOI":"10.1183\/23120541.00176-2023","article-title":"Cardiomyopathy as cause of death in Duchenne muscular dystrophy: A longitudinal observational study","volume":"9","author":"Lechner","year":"2023","journal-title":"ERJ Open Res."},{"key":"ref_297","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.nmd.2019.02.002","article-title":"Respiratory and upper limb function as outcome measures in ambulant and non- ambulant subjects with Duchenne muscular dystrophy: A prospective multicentre study","volume":"29","author":"Ricotti","year":"2019","journal-title":"Neuromuscul. Disord."},{"key":"ref_298","doi-asserted-by":"crossref","first-page":"2752","DOI":"10.1007\/s00415-019-09481-z","article-title":"Imaging respiratory muscle quality and function in Duchenne muscular dystrophy","volume":"266","author":"Barnard","year":"2019","journal-title":"J. Neurol."},{"key":"ref_299","doi-asserted-by":"crossref","unstructured":"Pennati, F., LoMauro, A., D\u2019Angelo, M.G., and Aliverti, A. (2019). Non-Invasive Respiratory Assessment in Duchenne Muscular Dystrophy: From Clinical Research to Outcome Measures. Life, 11.","DOI":"10.3390\/life11090947"},{"key":"ref_300","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3233\/JND-180326","article-title":"Echographic assessment of diaphragmatic function in Duchenne muscular dystrophy from childhood to adulthood","volume":"6","author":"Fayssoil","year":"2019","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_301","first-page":"5","article-title":"Autopsy study on the weight of the heart, liver, kidney and brain in Duchenne muscular dystrophy","volume":"38","author":"Moriuchi","year":"1991","journal-title":"Tokushima J. Exp. Med."},{"key":"ref_302","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1111\/apa.16649","article-title":"Metabolic assessment in children with neuromuscular disorders shows risk of liver enlargement, steatosis and fibrosis","volume":"112","author":"Naume","year":"2023","journal-title":"Acta Paediatr."},{"key":"ref_303","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1016\/j.nmd.2015.07.006","article-title":"Treatable renal failure found in non-ambulatory Duchenne muscular dystrophy patients","volume":"25","author":"Motoki","year":"2015","journal-title":"Neuromuscul. Disord."},{"key":"ref_304","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.nmd.2015.01.005","article-title":"Renal function in children and adolescents with Duchenne muscular dystrophy","volume":"25","author":"Braat","year":"2015","journal-title":"Neuromuscul. Disord."},{"key":"ref_305","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1007\/s00467-020-04587-3","article-title":"Kidney involvement and associated risk factors in children with Duchenne muscular dystrophy","volume":"35","author":"Kutluk","year":"2020","journal-title":"Pediatr. Nephrol."},{"key":"ref_306","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.nmd.2016.07.010","article-title":"Identifying evidence of cardio-renal syndrome in patients with Duchenne muscular dystrophy using cystatin C","volume":"26","author":"Villa","year":"2016","journal-title":"Neuromuscul. Disord."},{"key":"ref_307","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1002\/(SICI)1097-4598(199607)19:7<819::AID-MUS2>3.0.CO;2-C","article-title":"Urinary dysfunction in Duchenne muscular dystrophy","volume":"19","author":"Caress","year":"1996","journal-title":"Muscle Nerve"},{"key":"ref_308","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1136\/adc.88.4.347","article-title":"Bladder dysfunction in Duchenne muscular dystrophy","volume":"88","author":"MacLeod","year":"2003","journal-title":"Arch. Dis. Child."},{"key":"ref_309","doi-asserted-by":"crossref","unstructured":"Lionarons, J.M., de Groot, I.J.M., Fock, J.M., Klinkenberg, S., Vrijens, D.M.J., Vreugdenhil, A.C.E., Medici-van den Herik, E.G., Cuppen, I., Jaeger, B., and Niks, E.H. (2021). Prevalence of Bladder and Bowel Dysfunction in Duchenne Muscular Dystrophy Using the Childhood Bladder and Bowel Dysfunction Questionnaire. Life, 11.","DOI":"10.3390\/life11080772"},{"key":"ref_310","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1002\/mus.27077","article-title":"Prevalence of smooth muscle dysfunction among children with Duchenne muscular dystrophy","volume":"62","author":"Manokaran","year":"2020","journal-title":"Muscle Nerve"},{"key":"ref_311","first-page":"742","article-title":"Symptoms of upper gastrointestinal dysfunction in Duchenne muscular dystrophy: Case-control study","volume":"71","author":"Jaffe","year":"1990","journal-title":"Arch. Phys. Med. Rehabil."},{"key":"ref_312","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1111\/j.1572-0241.2005.41303.x","article-title":"Evolution of gastric electrical features and gastric emptying in children with Duchenne and Becker muscular dystrophy","volume":"100","author":"Borrelli","year":"2005","journal-title":"Am. J. Gastroenterol."},{"key":"ref_313","doi-asserted-by":"crossref","unstructured":"Lo Cascio, C.M., Goetze, O., Latshang, T.D., Bluemel, S., Frauenfelder, T., and Bloch, K.E. (2016). Gastrointestinal Dysfunction in Patients with Duchenne Muscular Dystrophy. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0163779"},{"key":"ref_314","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1002\/jbmr.410","article-title":"Mechanisms inducing low bone density in Duchenne muscular dystrophy in mice and humans","volume":"26","author":"Rufo","year":"2011","journal-title":"J. Bone Miner. Res."},{"key":"ref_315","doi-asserted-by":"crossref","first-page":"23","DOI":"10.3233\/PRM-160358","article-title":"Management of scoliosis in patients with Duchenne muscular dystrophy and spinal muscular atrophy: A literature review","volume":"9","author":"Garg","year":"2016","journal-title":"J. Pediatr. Rehabil. Med."},{"key":"ref_316","doi-asserted-by":"crossref","first-page":"411","DOI":"10.5312\/wjo.v14.i6.411","article-title":"Surgical and long-term functional outcomes of patients with Duchenne muscular dystrophy following spinal deformity correction","volume":"14","author":"Roberts","year":"2023","journal-title":"World J. Orthop."},{"key":"ref_317","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/dmcn.15711","article-title":"Survival of patients with Duchenne muscular dystrophy who underwent spinal deformity correction","volume":"66","author":"Arshad","year":"2024","journal-title":"Dev. Med. Child Neurol."},{"key":"ref_318","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/S0165-0173(99)00090-9","article-title":"Brain dystrophin, neurogenetics and mental retardation","volume":"32","author":"Mehler","year":"2000","journal-title":"Brain Res. Rev."},{"key":"ref_319","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/j.jpeds.2012.03.020","article-title":"Attention deficit hyperactivity disorder and cognitive function in Duchenne muscular dystrophy: Phenotype-genotype correlation","volume":"161","author":"Pane","year":"2012","journal-title":"J. Pediatr."},{"key":"ref_320","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1111\/dmcn.12922","article-title":"Neurodevelopmental, emotional, and behavioural problems in Duchenne muscular dystrophy in relation to underlying dystrophin gene mutations","volume":"58","author":"Ricotti","year":"2016","journal-title":"Dev. Med. Child Neurol."},{"key":"ref_321","doi-asserted-by":"crossref","first-page":"233","DOI":"10.23736\/S0026-4946.16.04380-2","article-title":"Autism spectrum disorders in children affected by Duchenne muscular dystrophy","volume":"70","author":"Parisi","year":"2018","journal-title":"Minerva Pediatr."},{"key":"ref_322","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1111\/dmcn.15481","article-title":"Global prevalence of intellectual developmental disorder in dystrophinopathies: A systematic review and meta-analysis","volume":"65","year":"2023","journal-title":"Dev. Med. Child Neurol."},{"key":"ref_323","doi-asserted-by":"crossref","unstructured":"Holland, A., and Ohlendieck, K. (2014). Proteomic profiling of the dystrophin-deficient mdx phenocopy of dystrophinopathy-associated cardiomyopathy. Biomed. Res. Int., 2014.","DOI":"10.1155\/2014\/246195"},{"key":"ref_324","doi-asserted-by":"crossref","unstructured":"Gowran, A., Brioschi, M., Rovina, D., Chiesa, M., Piacentini, L., Mallia, S., Banfi, C., Pompilio, G., and Santoro, R. (2021). Multiomic Approaches to Uncover the Complexities of Dystrophin-Associated Cardiomyopathy. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22168954"},{"key":"ref_325","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1007\/s11897-022-00541-6","article-title":"Biomarkers in Duchenne Muscular Dystrophy","volume":"19","author":"Jiang","year":"2022","journal-title":"Curr. Heart Fail. Rep."},{"key":"ref_326","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1097\/HCO.0000000000000611","article-title":"Multiomic approaches to delineate the pathogenesis of cardiac disease","volume":"34","author":"Matkovich","year":"2019","journal-title":"Curr. Opin. Cardiol."},{"key":"ref_327","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.5808\/gi.21002","article-title":"OMICS approaches in cardiovascular diseases: A mini review","volume":"19","author":"Sohag","year":"2021","journal-title":"Genom. Inform."},{"key":"ref_328","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1007\/s10741-019-09807-z","article-title":"Biomarkers in heart failure: The past, current and future","volume":"24","author":"Sarhene","year":"2019","journal-title":"Heart Fail. Rev."},{"key":"ref_329","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/s41569-020-00477-1","article-title":"Systems biology in cardiovascular disease: A multiomics approach","volume":"18","author":"Joshi","year":"2021","journal-title":"Nat. Rev. Cardiol."},{"key":"ref_330","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.bbadis.2004.04.002","article-title":"Drastic reduction in the luminal Ca2+-binding proteins calsequestrin and sarcalumenin in dystrophin-deficient cardiac muscle","volume":"1689","author":"Lohan","year":"2004","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_331","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1021\/pr800070p","article-title":"A combined metabolomic and proteomic investigation of the effects of a failure to express dystrophin in the mouse heart","volume":"7","author":"Gulston","year":"2008","journal-title":"J. Proteome Res."},{"key":"ref_332","doi-asserted-by":"crossref","unstructured":"Lewis, C., Jockusch, H., and Ohlendieck, K. (2010). Proteomic Profiling of the Dystrophin-Deficient MDX Heart Reveals Drastically Altered Levels of Key Metabolic and Contractile Proteins. J. Biomed. Biotechnol., 2010.","DOI":"10.1155\/2010\/648501"},{"key":"ref_333","doi-asserted-by":"crossref","unstructured":"Johnson, E.K., Zhang, L., Adams, M.E., Phillips, A., Freitas, M.A., Froehner, S.C., Green-Church, K.B., and Montanaro, F. (2012). Proteomic analysis reveals new cardiac-specific dystrophin-associated proteins. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0043515"},{"key":"ref_334","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1002\/pmic.201200578","article-title":"Proteomic profiling of cardiomyopathic tissue from the aged mdx model of Duchenne muscular dystrophy reveals a drastic decrease in laminin, nidogen and annexin","volume":"13","author":"Holland","year":"2013","journal-title":"Proteomics"},{"key":"ref_335","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.jprot.2016.03.011","article-title":"Proteomic analysis of dystrophin deficiency and associated changes in the aged mdx-4cv heart model of dystrophinopathy-related cardiomyopathy","volume":"145","author":"Murphy","year":"2016","journal-title":"J. Proteom."},{"key":"ref_336","doi-asserted-by":"crossref","first-page":"E10763","DOI":"10.1073\/pnas.1712623114","article-title":"Transient receptor potential channel 6 regulates abnormal cardiac S-nitrosylation in Duchenne muscular dystrophy","volume":"114","author":"Chung","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_337","doi-asserted-by":"crossref","first-page":"101516","DOI":"10.1016\/j.isci.2020.101516","article-title":"Progressive Proteome Changes in the Myocardium of a Pig Model for Duchenne Muscular Dystrophy","volume":"23","author":"Tamiyakul","year":"2020","journal-title":"iScience"},{"key":"ref_338","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1093\/cvr\/cvm089","article-title":"Dystrophic cardiomyopathy: Amplification of cellular damage by Ca2+ signalling and reactive oxygen species-generating pathways","volume":"77","author":"Jung","year":"2008","journal-title":"Cardiovasc. Res."},{"key":"ref_339","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1161\/01.RES.72.2.349","article-title":"Dystrophin-glycoprotein complex and laminin colocalize to the sarcolemma and transverse tubules of cardiac muscle","volume":"72","author":"Klietsch","year":"1993","journal-title":"Circ. Res."},{"key":"ref_340","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1093\/hmg\/ddab133","article-title":"Proteomic analysis identifies key differences in the cardiac interactomes of dystrophin and micro-dystrophin","volume":"30","author":"Wang","year":"2021","journal-title":"Hum. Mol. Genet."},{"key":"ref_341","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s12014-018-9212-2","article-title":"Proteomic profiling of liver tissue from the mdx-4cv mouse model of Duchenne muscular dystrophy","volume":"15","author":"Murphy","year":"2018","journal-title":"Clin. Proteom."},{"key":"ref_342","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1080\/14789450.2020.1732214","article-title":"Proteomic profiling of fatty acid binding proteins in muscular dystrophy","volume":"17","author":"Dowling","year":"2020","journal-title":"Expert Rev. Proteom."},{"key":"ref_343","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.3892\/ijmm.2017.2952","article-title":"Proteomic profiling of mdx-4cv serum reveals highly elevated levels of the inflammation-induced plasma marker haptoglobin in muscular dystrophy","volume":"39","author":"Murphy","year":"2017","journal-title":"Int. J. Mol. Med."},{"key":"ref_344","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1016\/j.dib.2018.10.082","article-title":"Dataset on the comparative proteomic profiling of mouse saliva and serum from wild type versus the dystrophic mdx-4cv mouse model of dystrophinopathy","volume":"21","author":"Murphy","year":"2018","journal-title":"Data Brief."},{"key":"ref_345","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1080\/14789450.2018.1429923","article-title":"Proteomic serum biomarkers for neuromuscular diseases","volume":"15","author":"Murphy","year":"2018","journal-title":"Expert Rev. Proteom."},{"key":"ref_346","doi-asserted-by":"crossref","unstructured":"Dowling, P., Zweyer, M., Raucamp, M., Henry, M., Meleady, P., Swandulla, D., and Ohlendieck, K. (2020). Proteomic and cell biological profiling of the renal phenotype of the mdx-4cv mouse model of Duchenne muscular dystrophy. Eur. J. Cell Biol., 99.","DOI":"10.1016\/j.ejcb.2019.151059"},{"key":"ref_347","doi-asserted-by":"crossref","first-page":"105067","DOI":"10.1016\/j.dib.2019.105067","article-title":"Dataset on the mass spectrometry-based proteomic profiling of the kidney from wild type and the dystrophic mdx-4cv mouse model of X-linked muscular dystrophy","volume":"28","author":"Dowling","year":"2020","journal-title":"Data Brief"},{"key":"ref_348","doi-asserted-by":"crossref","first-page":"6458","DOI":"10.1093\/hmg\/ddu366","article-title":"Discovery of serum protein biomarkers in the mdx mouse model and cross-species comparison to Duchenne muscular dystrophy patients","volume":"23","author":"Hathout","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"ref_349","doi-asserted-by":"crossref","first-page":"17014","DOI":"10.1038\/srep17014","article-title":"Identification of novel, therapy-responsive protein biomarkers in a mouse model of Duchenne muscular dystrophy by aptamer-based serum proteomics","volume":"5","author":"McClorey","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_350","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1002\/jcsm.12304","article-title":"Tracking disease progression non-invasively in Duchenne and Becker muscular dystrophies","volume":"9","author":"Spitali","year":"2018","journal-title":"J. Cachexia Sarcopenia Muscle"},{"key":"ref_351","doi-asserted-by":"crossref","unstructured":"Parolo, S., Marchetti, L., Lauria, M., Misselbeck, K., Scott-Boyer, M.P., Caberlotto, L., and Priami, C. (2018). Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0194225"},{"key":"ref_352","doi-asserted-by":"crossref","first-page":"e1010966","DOI":"10.1080\/21675511.2015.1010966","article-title":"The immune system in Duchenne muscular dystrophy: Friend or foe","volume":"3","author":"Villalta","year":"2015","journal-title":"Rare Dis."},{"key":"ref_353","doi-asserted-by":"crossref","first-page":"299rv4","DOI":"10.1126\/scitranslmed.aaa7322","article-title":"Immune-mediated pathology in Duchenne muscular dystrophy","volume":"7","author":"Rosenberg","year":"2015","journal-title":"Sci. Transl. Med."},{"key":"ref_354","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1002\/cphy.c170052","article-title":"Immunobiology of Inherited Muscular Dystrophies","volume":"8","author":"Tidball","year":"2018","journal-title":"Compr. Physiol."},{"key":"ref_355","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1038\/mt.2016.162","article-title":"Therapeutic Potential of Immunoproteasome Inhibition in Duchenne Muscular Dystrophy","volume":"24","author":"Farini","year":"2014","journal-title":"Mol. Ther."},{"key":"ref_356","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1093\/hmg\/ddu735","article-title":"Toll-like receptor 4 ablation in mdx mice reveals innate immunity as a therapeutic target in Duchenne muscular dystrophy","volume":"24","author":"Giordano","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"ref_357","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.3389\/fimmu.2019.02131","article-title":"Immunophenotype of a Rat Model of Duchenne\u2019s Disease and Demonstration of Improved Muscle Strength After Anti-CD45RC Antibody Treatment","volume":"10","author":"Ouisse","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_358","doi-asserted-by":"crossref","unstructured":"Tripodi, L., Molinaro, D., Fortunato, F., Mella, C., Cassani, B., Torrente, Y., and Farini, A. (2022). Immunoproteasome Inhibition Ameliorates Aged Dystrophic Mouse Muscle Environment. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232314657"},{"key":"ref_359","doi-asserted-by":"crossref","unstructured":"Tripodi, L., Villa, C., Molinaro, D., Torrente, Y., and Farini, A. (2021). The Immune System in Duchenne Muscular Dystrophy Pathogenesis. Biomedicines, 9.","DOI":"10.3390\/biomedicines9101447"},{"key":"ref_360","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.15252\/emmm.201403967","article-title":"Inflammatory monocytes promote progression of Duchenne muscular dystrophy and can be therapeutically targeted via CCR2","volume":"6","author":"Mojumdar","year":"2014","journal-title":"EMBO Mol. Med."},{"key":"ref_361","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1002\/path.4689","article-title":"Divergent impact of Toll-like receptor 2 deficiency on repair mechanisms in healthy muscle versus Duchenne muscular dystrophy","volume":"239","author":"Mojumdar","year":"2016","journal-title":"J. Pathol."},{"key":"ref_362","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1002\/path.5016","article-title":"Targeting early PKC\u03b8-dependent T-cell infiltration of dystrophic muscle reduces disease severity in a mouse model of muscular dystrophy","volume":"244","author":"Benedetti","year":"2018","journal-title":"J. Pathol."},{"key":"ref_363","doi-asserted-by":"crossref","first-page":"1202834","DOI":"10.3389\/fimmu.2023.1202834","article-title":"T cell biology in neuromuscular disorders: A focus on Duchenne Muscular Dystrophy and Amyotrophic Lateral Sclerosis","volume":"14","author":"Lemos","year":"2023","journal-title":"Front. Immunol."},{"key":"ref_364","doi-asserted-by":"crossref","first-page":"1183066","DOI":"10.3389\/fimmu.2023.1183066","article-title":"Trained immunity as a potential target for therapeutic immunomodulation in Duchenne muscular dystrophy","volume":"14","author":"Petrof","year":"2023","journal-title":"Front. Immunol."},{"key":"ref_365","doi-asserted-by":"crossref","first-page":"130807","DOI":"10.1172\/jci.insight.130807","article-title":"Splenic Ly6Chi monocytes are critical players in dystrophic muscle injury and repair","volume":"5","author":"Rizzo","year":"2020","journal-title":"JCI Insight"},{"key":"ref_366","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/nri1669","article-title":"Structure and function of the spleen","volume":"5","author":"Mebius","year":"2005","journal-title":"Nat. Rev. Immunol."},{"key":"ref_367","doi-asserted-by":"crossref","first-page":"eaau6085","DOI":"10.1126\/sciimmunol.aau6085","article-title":"Structure and function of the immune system in the spleen","volume":"4","author":"Lewis","year":"2019","journal-title":"Sci. Immunol."},{"key":"ref_368","doi-asserted-by":"crossref","first-page":"101500","DOI":"10.1016\/j.isci.2020.101500","article-title":"Proteome-wide Changes in the mdx-4cv Spleen due to Pathophysiological Cross Talk with Dystrophin-Deficient Skeletal Muscle","volume":"23","author":"Dowling","year":"2020","journal-title":"iScience"},{"key":"ref_369","first-page":"9627","article-title":"Proteomic profiling of the interface between the stomach wall and the pancreas in dystrophinopathy","volume":"31","author":"Dowling","year":"2021","journal-title":"Eur. J. Transl. Myol."},{"key":"ref_370","doi-asserted-by":"crossref","first-page":"11553","DOI":"10.4081\/ejtm.2023.11553","article-title":"Mass spectrometry-based proteomic characterization of the middle-aged mouse brain for animal model research of neuromuscular diseases","volume":"33","author":"Dowling","year":"2023","journal-title":"Eur. J. Transl. Myol."},{"key":"ref_371","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s12014-015-9099-0","article-title":"Label-free mass spectrometric analysis reveals complex changes in the brain proteome from the mdx-4cv mouse model of Duchenne muscular dystrophy","volume":"12","author":"Murphy","year":"2015","journal-title":"Clin. Proteom."},{"key":"ref_372","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/978-1-4939-7374-3_7","article-title":"Proteomic Profiling of the Dystrophin-Deficient Brain","volume":"1687","author":"Murphy","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref_373","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.tins.2015.04.003","article-title":"Glial fibrillary acidic protein: From intermediate filament assembly and gliosis to neurobiomarker","volume":"38","author":"Yang","year":"2015","journal-title":"Trends Neurosci."},{"key":"ref_374","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41593-020-00783-4","article-title":"Reactive astrocyte nomenclature, definitions, and future directions","volume":"24","author":"Escartin","year":"2021","journal-title":"Nat. Neurosci."},{"key":"ref_375","doi-asserted-by":"crossref","unstructured":"Jurga, A.M., Paleczna, M., Kadluczka, J., and Kuter, K.Z. (2021). Beyond the GFAP-Astrocyte Protein Markers in the Brain. Biomolecules, 11.","DOI":"10.3390\/biom11091361"},{"key":"ref_376","doi-asserted-by":"crossref","first-page":"11555","DOI":"10.4081\/ejtm.2023.11555","article-title":"Proteomic profiling of the brain from the wobbler mouse model of amyotrophic lateral sclerosis reveals elevated levels of the astrogliosis marker glial fibrillary acidic protein","volume":"33","author":"Murphy","year":"2023","journal-title":"Eur. J. Transl. Myol."},{"key":"ref_377","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1002\/jcsm.12914","article-title":"Investigating the role of dystrophin isoform deficiency in motor function in Duchenne muscular dystrophy","volume":"13","author":"Chesshyre","year":"2022","journal-title":"J. Cachexia Sarcopenia Muscle"},{"key":"ref_378","doi-asserted-by":"crossref","unstructured":"De Stefano, M.E., Ferretti, V., and Mozzetta, C. (2022). Synaptic alterations as a neurodevelopmental trait of Duchenne muscular dystrophy. Neurobiol. Dis., 168.","DOI":"10.1016\/j.nbd.2022.105718"},{"key":"ref_379","doi-asserted-by":"crossref","unstructured":"Wijekoon, N., Gonawala, L., Ratnayake, P., Amaratunga, D., Hathout, Y., Mohan, C., Steinbusch, H.W.M., Dalal, A., Hoffman, E.P., and de Silva, K.R.D. (2023). Duchenne Muscular Dystrophy from Brain to Muscle: The Role of Brain Dystrophin Isoforms in Motor Functions. J. Clin. Med., 12.","DOI":"10.3390\/jcm12175637"},{"key":"ref_380","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1097\/CND.0000000000000436","article-title":"DMD Gene and Dystrophinopathy Phenotypes Associated with Mutations: A Systematic Review for Clinicians","volume":"24","author":"Andrews","year":"2023","journal-title":"J. Clin. Neuromuscul. Dis."},{"key":"ref_381","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/164_2019_256","article-title":"Pharmacotherapy of Duchenne Muscular Dystrophy","volume":"261","author":"Hoffman","year":"2020","journal-title":"Handb. Exp. Pharmacol."},{"key":"ref_382","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1080\/14656566.2020.1732350","article-title":"New and emerging pharmacotherapy for duchenne muscular dystrophy: A focus on synthetic therapeutics","volume":"21","author":"Grages","year":"2020","journal-title":"Expert Opin. Pharmacother."},{"key":"ref_383","doi-asserted-by":"crossref","first-page":"950651","DOI":"10.3389\/fphar.2022.950651","article-title":"Drug development progress in duchenne muscular dystrophy","volume":"13","author":"Deng","year":"2022","journal-title":"Front. Pharmacol."},{"key":"ref_384","doi-asserted-by":"crossref","unstructured":"Rawls, A., Diviak, B.K., Smith, C.I., Severson, G.W., Acosta, S.A., and Wilson-Rawls, J. (2023). Pharmacotherapeutic Approaches to Treatment of Muscular Dystrophies. Biomolecules, 13.","DOI":"10.3390\/biom13101536"},{"key":"ref_385","doi-asserted-by":"crossref","unstructured":"Fortunato, F., Rossi, R., Falzarano, M.S., and Ferlini, A. (2021). Innovative Therapeutic Approaches for Duchenne Muscular Dystrophy. J. Clin. Med., 10.","DOI":"10.3390\/jcm10040820"},{"key":"ref_386","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/S1474-4422(22)00125-9","article-title":"Emerging therapies for Duchenne muscular dystrophy","volume":"21","author":"Markati","year":"2022","journal-title":"Lancet Neurol."},{"key":"ref_387","doi-asserted-by":"crossref","unstructured":"Chung Liang, L., Sulaiman, N., and Yazid, M.D. (2022). A Decade of Progress in Gene Targeted Therapeutic Strategies in Duchenne Muscular Dystrophy: A Systematic Review. Front. Bioeng. Biotechnol., 10.","DOI":"10.3389\/fbioe.2022.833833"},{"key":"ref_388","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.1007\/s00415-023-11796-x","article-title":"Duchenne muscular dystrophy: Pathogenesis and promising therapies","volume":"270","author":"Chang","year":"2023","journal-title":"J. Neurol."},{"key":"ref_389","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1089\/hum.2023.29242.ddu","article-title":"Duchenne Muscular Dystrophy Gene Therapy in 2023: Status, Perspective, and Beyond","volume":"34","author":"Duan","year":"2023","journal-title":"Hum. Gene Ther."},{"key":"ref_390","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1001\/jamaneurol.2020.1264","article-title":"Safety, Tolerability, and Efficacy of Viltolarsen in Boys With Duchenne Muscular Dystrophy Amenable to Exon 53 Skipping: A Phase 2 Randomized Clinical Trial","volume":"77","author":"Clemens","year":"2020","journal-title":"JAMA Neurol."},{"key":"ref_391","doi-asserted-by":"crossref","first-page":"S383","DOI":"10.3233\/JND-210696","article-title":"Interrogation of Dystrophin and Dystroglycan Complex Protein Turnover After Exon Skipping Therapy","volume":"8","author":"Novak","year":"2021","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_392","doi-asserted-by":"crossref","unstructured":"Eser, G., and Topalo\u011flu, H. (2022). Current Outline of Exon Skipping Trials in Duchenne Muscular Dystrophy. Genes, 13.","DOI":"10.3390\/genes13071241"},{"key":"ref_393","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.nmd.2023.03.008","article-title":"Safety, tolerability and pharmacokinetics of eteplirsen in young boys aged 6-48 months with Duchenne muscular dystrophy amenable to exon 51 skipping","volume":"33","author":"Mercuri","year":"2023","journal-title":"Neuromuscul. Disord."},{"key":"ref_394","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1146\/annurev-med-081117-010451","article-title":"CRISPR Correction of Duchenne Muscular Dystrophy","volume":"70","author":"Min","year":"2019","journal-title":"Annu. Rev. Med."},{"key":"ref_395","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/s41434-021-00222-4","article-title":"Genome editing for Duchenne muscular dystrophy: A glimpse of the future?","volume":"28","author":"Kupatt","year":"2021","journal-title":"Gene Ther."},{"key":"ref_396","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1089\/hum.2023.053","article-title":"CRISPR- Editing Therapy for Duchenne Muscular Dystrophy","volume":"34","author":"Chemello","year":"2023","journal-title":"Hum. Gene Ther."},{"key":"ref_397","first-page":"43","article-title":"Read-through approach for stop mutations in Duchenne muscular dystrophy. An update","volume":"40","author":"Politano","year":"2021","journal-title":"Acta Myol."},{"key":"ref_398","doi-asserted-by":"crossref","first-page":"139","DOI":"10.2174\/156652312800840603","article-title":"Gene replacement therapies for duchenne muscular dystrophy using adeno-associated viral vectors","volume":"12","author":"Seto","year":"2012","journal-title":"Curr. Gene Ther."},{"key":"ref_399","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1089\/hum.2015.107","article-title":"Perspective on Adeno-Associated Virus Capsid Modification for Duchenne Muscular Dystrophy Gene Therapy","volume":"26","author":"Nance","year":"2015","journal-title":"Hum. Gene Ther."},{"key":"ref_400","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.1016\/j.ymthe.2018.07.011","article-title":"Systemic AAV Micro-dystrophin Gene Therapy for Duchenne Muscular Dystrophy","volume":"26","author":"Duan","year":"2018","journal-title":"Mol. Ther."},{"key":"ref_401","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1001\/jamaneurol.2020.1484","article-title":"Assessment of Systemic Delivery of rAAVrh74.MHCK7.micro-dystrophin in Children with Duchenne Muscular Dystrophy: A Nonrandomized Controlled Trial","volume":"77","author":"Mendell","year":"2020","journal-title":"JAMA Neurol."},{"key":"ref_402","doi-asserted-by":"crossref","unstructured":"Matsuzaka, Y., Hirai, Y., Hashido, K., and Okada, T. (2022). Therapeutic Application of Extracellular Vesicles-Capsulated Adeno-Associated Virus Vector via nSMase2\/Smpd3, Satellite, and Immune Cells in Duchenne Muscular Dystrophy. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031551"},{"key":"ref_403","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1038\/s41598-020-58737-6","article-title":"High-throughput identification of post-transcriptional utrophin up-regulators for Duchenne muscle dystrophy (DMD) therapy","volume":"10","author":"Loro","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_404","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1111\/nan.12735","article-title":"Utrophin modulator drugs as potential therapies for Duchenne and Becker muscular dystrophies","volume":"47","year":"2021","journal-title":"Neuropathol. Appl. Neurobiol."},{"key":"ref_405","doi-asserted-by":"crossref","first-page":"113431","DOI":"10.1016\/j.ejmech.2021.113431","article-title":"Discovery and mechanism of action studies of 4,6-diphenylpyrimidine-2-carbohydrazides as utrophin modulators for the treatment of Duchenne muscular dystrophy","volume":"220","author":"Vuorinen","year":"2021","journal-title":"Eur. J. Med. Chem."},{"key":"ref_406","doi-asserted-by":"crossref","first-page":"112908","DOI":"10.1016\/j.yexcr.2021.112908","article-title":"Challenges in cell transplantation for muscular dystrophy","volume":"409","author":"Galli","year":"2021","journal-title":"Exp. Cell Res."},{"key":"ref_407","doi-asserted-by":"crossref","first-page":"702547","DOI":"10.3389\/fgene.2021.702547","article-title":"Myogenic Cell Transplantation in Genetic and Acquired Diseases of Skeletal Muscle","volume":"12","author":"Boyer","year":"2021","journal-title":"Front. Genet."},{"key":"ref_408","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1007\/s12015-020-10100-y","article-title":"Systemic cell therapy for muscular dystrophies: The ultimate transplantable muscle progenitor cell and current challenges for clinical efficacy","volume":"17","author":"Ausems","year":"2021","journal-title":"Stem Cell Rev. Rep."},{"key":"ref_409","doi-asserted-by":"crossref","first-page":"1190524","DOI":"10.3389\/fphys.2023.1190524","article-title":"Duchenne muscular dystrophy disease severity impacts skeletal muscle progenitor cells systemic delivery","volume":"14","author":"Saleh","year":"2023","journal-title":"Front. Physiol."},{"key":"ref_410","doi-asserted-by":"crossref","first-page":"11154","DOI":"10.3390\/molecules200611154","article-title":"Non-Invasive Biomarkers for Duchenne Muscular Dystrophy and Carrier Detection","volume":"20","year":"2015","journal-title":"Molecules"},{"key":"ref_411","doi-asserted-by":"crossref","first-page":"987","DOI":"10.3233\/JND-221666","article-title":"Biomarkers in Duchenne Muscular Dystrophy: Current Status and Future Directions","volume":"10","author":"Fortunato","year":"2023","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_412","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/978-1-0716-2831-7_12","article-title":"Proteomic Identification of Saliva Proteins as Noninvasive Diagnostic Biomarkers","volume":"2596","author":"Dowling","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_413","doi-asserted-by":"crossref","first-page":"169","DOI":"10.2217\/bmm.12.96","article-title":"Proteomic identification of biomarkers of skeletal muscle disorders","volume":"7","author":"Ohlendieck","year":"2013","journal-title":"Biomark. Med."},{"key":"ref_414","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.pmr.2012.06.006","article-title":"Muscle biopsy evaluation in neuromuscular disorders","volume":"23","author":"Joyce","year":"2012","journal-title":"Med. Rehabil. Clin. N. Am."},{"key":"ref_415","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1007\/s00415-011-6193-8","article-title":"Muscle biopsy","volume":"259","author":"Meola","year":"2012","journal-title":"J. Neurol."},{"key":"ref_416","first-page":"51812","article-title":"Human skeletal muscle biopsy procedures using the modified Bergstr\u00f6m technique","volume":"10","author":"Shanely","year":"2014","journal-title":"J. Vis. Exp."},{"key":"ref_417","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1093\/jnen\/nlaa046","article-title":"What Every Neuropathologist Needs to Know: The Muscle Biopsy","volume":"79","author":"Nix","year":"2020","journal-title":"J. Neuropathol. Exp. Neurol."},{"key":"ref_418","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1515\/CCLM.2010.179","article-title":"Biochemical markers of muscular damage","volume":"48","author":"Brancaccio","year":"2010","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_419","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1515\/cclm-2018-0656","article-title":"Diagnostic biomarkers of muscle injury and exertional rhabdomyolysis","volume":"57","author":"Lippi","year":"2018","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_420","doi-asserted-by":"crossref","first-page":"241","DOI":"10.3233\/JND-140066","article-title":"Muscle-Derived Proteins as Serum Biomarkers for Monitoring Disease Progression in Three Forms of Muscular Dystrophy","volume":"2","author":"Burch","year":"2015","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_421","first-page":"1","article-title":"Biomarkers of Duchenne muscular dystrophy: Current findings","volume":"8","author":"Szigyarto","year":"2018","journal-title":"Degener. Neurol. Neuromuscul. Dis."},{"key":"ref_422","doi-asserted-by":"crossref","first-page":"dmm043638","DOI":"10.1242\/dmm.043638","article-title":"Biomarkers for Duchenne muscular dystrophy: Myonecrosis, inflammation and oxidative stress","volume":"13","author":"Grounds","year":"2020","journal-title":"Dis. Model Mech."},{"key":"ref_423","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1080\/14789450.2021.2017776","article-title":"Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle","volume":"18","author":"Dowling","year":"2021","journal-title":"Expert Rev. Proteom."},{"key":"ref_424","doi-asserted-by":"crossref","unstructured":"Rossi, R., Johansson, C., Heywood, W., Vinette, H., Jensen, G., Tegel, H., Jim\u00e9nez-Requena, A., Torelli, S., Al-Khalili Szigyarto, C., and Ferlini, A. (2023). A Proof of Principle Proteomic Study Detects Dystrophin in Human Plasma: Implications in DMD Diagnosis and Clinical Monitoring. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24065215"},{"key":"ref_425","doi-asserted-by":"crossref","unstructured":"Ogundele, M., Zhang, J.S., Goswami, M.V., Barbieri, M.L., Dang, U.J., Novak, J.S., Hoffman, E.P., Nagaraju, K., Cinrg-Dnhs Investigators, and Hathout, Y. (2021). Validation of Chemokine Biomarkers in Duchenne Muscular Dystrophy. Life, 11.","DOI":"10.3390\/life11080827"},{"key":"ref_426","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s12014-023-09412-1","article-title":"Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers","volume":"20","author":"Johansson","year":"2023","journal-title":"Clin. Proteom."},{"key":"ref_427","doi-asserted-by":"crossref","first-page":"4916","DOI":"10.1093\/hmg\/ddv214","article-title":"Serum proteomic profiling reveals fragments of MYOM3 as potential biomarkers for monitoring the outcome of therapeutic interventions in muscular dystrophies","volume":"24","author":"Rouillon","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"ref_428","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/j.nmd.2014.03.012","article-title":"Proteomics profiling of urine reveals specific titin fragments as biomarkers of Duchenne muscular dystrophy","volume":"24","author":"Rouillon","year":"2014","journal-title":"Neuromuscul. Disord."},{"key":"ref_429","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.nmd.2017.05.009","article-title":"Dramatic elevation in urinary amino terminal titin fragment excretion quantified by immunoassay in Duchenne muscular dystrophy patients and in dystrophin deficient rodents","volume":"27","author":"Robertson","year":"2017","journal-title":"Neuromuscul. Disord."},{"key":"ref_430","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1039\/C9MO00182D","article-title":"Identification of marker proteins of muscular dystrophy in the urine proteome from the mdx-4cv model of dystrophinopathy","volume":"16","author":"Gargan","year":"2020","journal-title":"Mol. Omics"},{"key":"ref_431","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/bs.acc.2019.01.001","article-title":"Titin fragment in urine: A noninvasive biomarker of muscle degradation","volume":"90","author":"Matsuo","year":"2019","journal-title":"Adv. Clin. Chem."},{"key":"ref_432","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.nmd.2023.02.003","article-title":"Urine titin as a novel biomarker for Duchenne muscular dystrophy","volume":"33","author":"Ishii","year":"2023","journal-title":"Neuromuscul. Disord."},{"key":"ref_433","doi-asserted-by":"crossref","unstructured":"Murphy, S., Zweyer, M., Mundegar, R.R., Swandulla, D., and Ohlendieck, K. (2018). Proteomic identification of elevated saliva kallikrein levels in the mdx-4cv mouse model of Duchenne muscular dystrophy. Biochem. Biophys. Rep., 18.","DOI":"10.1016\/j.bbrep.2018.05.006"},{"key":"ref_434","doi-asserted-by":"crossref","unstructured":"Olivier, M., Asmis, R., Hawkins, G.A., Howard, T.D., and Cox, L.A. (2019). The Need for Multi-Omics Biomarker Signatures in Precision Medicine. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20194781"},{"key":"ref_435","doi-asserted-by":"crossref","unstructured":"Wang, R.C., and Wang, Z. (2023). Precision Medicine: Disease Subtyping and Tailored Treatment. Cancers, 15.","DOI":"10.3390\/cancers15153837"},{"key":"ref_436","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1074\/mcp.R500014-MCP200","article-title":"Integrating cytomics and proteomics","volume":"5","author":"Bernas","year":"2006","journal-title":"Mol. Cell. Proteom."},{"key":"ref_437","doi-asserted-by":"crossref","first-page":"263","DOI":"10.2174\/138920008783884731","article-title":"Cytomics","volume":"9","author":"Gomase","year":"2008","journal-title":"Curr. Drug Metab."},{"key":"ref_438","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nrm3970","article-title":"Multidimensional proteomics for cell biology","volume":"16","author":"Larance","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_439","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1016\/j.jpha.2023.06.011","article-title":"Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective","volume":"13","author":"Lim","year":"2023","journal-title":"J. Pharm. Anal."},{"key":"ref_440","doi-asserted-by":"crossref","unstructured":"Alto, S.I., Chang, C.N., Brown, K., Kioussi, C., and Filtz, T.M. (2021). Gene Expression Profiling of Skeletal Muscles. Genes, 12.","DOI":"10.1101\/2021.02.17.431599"},{"key":"ref_441","doi-asserted-by":"crossref","unstructured":"Erbe, L.S., Hoffjan, S., Jan\u00dfen, S., Kneifel, M., Krause, K., Gerding, W.M., D\u00f6ring, K., G\u00fcttsches, A.K., Roos, A., and Buena Atienza, E. (2023). Exome Sequencing and Optical Genome Mapping in Molecularly Unsolved Cases of Duchenne Muscular Dystrophy: Identification of a Causative X-Chromosomal Inversion Disrupting the DMD Gene. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241914716"},{"key":"ref_442","doi-asserted-by":"crossref","unstructured":"Pluta, N., von Moers, A., Pechmann, A., Stenzel, W., Goebel, H.H., Atlan, D., Wolf, B., Nanda, I., Zaum, A.K., and Rost, S. (2023). Whole-Genome Sequencing Identified New Structural Variations in the DMD Gene That Cause Duchenne Muscular Dystrophy in Two Girls. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241713567"},{"key":"ref_443","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1007\/978-1-4939-9240-9_26","article-title":"A Bioinformatic Toolkit for Single-Cell mRNA Analysis","volume":"1979","author":"Becker","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_444","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: The teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_445","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","article-title":"Exploring tissue architecture using spatial transcriptomics","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"ref_446","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-3-031-05460-0_5","article-title":"Post-translational Modification in Muscular Dystrophies","volume":"1382","author":"Saccone","year":"2022","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_447","doi-asserted-by":"crossref","first-page":"151959","DOI":"10.1016\/j.acthis.2022.151959","article-title":"The location of protein oxidation in dystrophic skeletal muscle from the mdx mouse model of Duchenne muscular dystrophy","volume":"124","author":"Iwasaki","year":"2022","journal-title":"Acta Histochem."},{"key":"ref_448","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1186\/s13023-023-02885-1","article-title":"The metabolomic plasma profile of patients with Duchenne muscular dystrophy: Providing new evidence for its pathogenesis","volume":"18","author":"Xu","year":"2023","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_449","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1038\/s41598-021-81090-1","article-title":"Muscle metabolic remodelling patterns in Duchenne muscular dystrophy revealed by ultra-high-resolution mass spectrometry imaging","volume":"11","author":"Dabaj","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_450","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1093\/hmg\/ddz309","article-title":"Longitudinal metabolomic analysis of plasma enables modeling disease progression in Duchenne muscular dystrophy mouse models","volume":"29","author":"Tsonaka","year":"2020","journal-title":"Hum. Mol. Genet."},{"key":"ref_451","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s13395-017-0135-9","article-title":"Increased plasma lipid levels exacerbate muscle pathology in the mdx mouse model of Duchenne muscular dystrophy","volume":"7","author":"Milad","year":"2017","journal-title":"Skelet. Muscle"},{"key":"ref_452","doi-asserted-by":"crossref","first-page":"12993","DOI":"10.1038\/s41598-021-92406-6","article-title":"Plasma lipidomic analysis shows a disease progression signature in mdx mice","volume":"11","author":"Tsonaka","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_453","doi-asserted-by":"crossref","first-page":"6445","DOI":"10.1096\/fj.201701151RRR","article-title":"Galectin-3 and N-acetylglucosamine promote myogenesis and improve skeletal muscle function in the mdx model of Duchenne muscular dystrophy","volume":"32","author":"Rancourt","year":"2018","journal-title":"FASEB J."},{"key":"ref_454","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1038\/s41590-022-01309-9","article-title":"A guide to systems-level immunomics","volume":"23","author":"Bonaguro","year":"2022","journal-title":"Nat. Immunol."},{"key":"ref_455","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/s41589-020-00698-y","article-title":"Cell type-selective secretome profiling in vivo","volume":"17","author":"Wei","year":"2021","journal-title":"Nat. Chem. Biol."},{"key":"ref_456","first-page":"603","article-title":"Are histochemistry and cytochemistry \u2018Omics\u2019?","volume":"35","author":"Coulton","year":"2004","journal-title":"J. Mol. Histol."},{"key":"ref_457","doi-asserted-by":"crossref","unstructured":"Robinson, J.P., Ostafe, R., Iyengar, S.N., Rajwa, B., and Fischer, R. (2023). Flow Cytometry: The Next Revolution. Cells, 12.","DOI":"10.3390\/cells12141875"},{"key":"ref_458","doi-asserted-by":"crossref","unstructured":"Ercan, H., Resch, U., Hsu, F., Mitulovic, G., Bileck, A., Gerner, C., Yang, J.W., Geiger, M., Miller, I., and Zellner, M. (2023). A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection. Cells, 12.","DOI":"10.3390\/cells12050747"},{"key":"ref_459","doi-asserted-by":"crossref","first-page":"3510","DOI":"10.1021\/acs.jproteome.0c00332","article-title":"Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data","volume":"19","author":"Schaffer","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_460","doi-asserted-by":"crossref","first-page":"4867","DOI":"10.1007\/s00018-021-03821-x","article-title":"Therapeutic aspects of cell signaling and communication in Duchenne muscular dystrophy","volume":"78","author":"Starosta","year":"2021","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_461","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1038\/s41587-022-01302-5","article-title":"Deep Visual Proteomics defines single-cell identity and heterogeneity","volume":"40","author":"Mund","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_462","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1038\/s41592-023-02007-6","article-title":"Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome","volume":"20","author":"Rosenberger","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_463","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aan6826","article-title":"Single-cell epigenomics: Recording the past and predicting the future","volume":"358","author":"Kelsey","year":"2017","journal-title":"Science"},{"key":"ref_464","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1161\/CIRCRESAHA.118.310998","article-title":"Epigenomics: Technologies and Applications","volume":"122","author":"Wang","year":"2018","journal-title":"Circ. Res."},{"key":"ref_465","doi-asserted-by":"crossref","first-page":"981","DOI":"10.2217\/epi-2021-0153","article-title":"Epigenomics in the single cell era, an important read out for genome function and cell identity","volume":"13","author":"Pinheiro","year":"2021","journal-title":"Epigenomics"},{"key":"ref_466","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.ymeth.2020.06.022","article-title":"Modern epigenetics methods in biological research","volume":"187","author":"Li","year":"2021","journal-title":"Methods"},{"key":"ref_467","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/bs.ctdb.2017.08.002","article-title":"Epigenetic Regulation of Adult Myogenesis","volume":"126","author":"Robinson","year":"2018","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_468","doi-asserted-by":"crossref","unstructured":"Plaza-Diaz, J., Izquierdo, D., Torres-Martos, \u00c1., Baig, A.T., Aguilera, C.M., and Ruiz-Ojeda, F.J. (2022). Impact of Physical Activity and Exercise on the Epigenome in Skeletal Muscle and Effects on Systemic Metabolism. Biomedicines, 10.","DOI":"10.3390\/biomedicines10010126"},{"key":"ref_469","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13395-020-00259-w","article-title":"Epigenetic regulation of satellite cell fate during skeletal muscle regeneration","volume":"11","author":"Massenet","year":"2021","journal-title":"Skelet. Muscle"},{"key":"ref_470","doi-asserted-by":"crossref","first-page":"547","DOI":"10.2217\/epi.14.36","article-title":"Histone deacetylase inhibitors: A potential epigenetic treatment for Duchenne muscular dystrophy","volume":"6","author":"Consalvi","year":"2014","journal-title":"Epigenomics"},{"key":"ref_471","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.nmd.2022.12.003","article-title":"The discovery of the DNA methylation episignature for Duchenne muscular dystrophy","volume":"33","author":"Schreyer","year":"2023","journal-title":"Neuromuscul. Disord."},{"key":"ref_472","doi-asserted-by":"crossref","unstructured":"Sandon\u00e0, M., Cavioli, G., Renzini, A., Cedola, A., Gigli, G., Coletti, D., McKinsey, T.A., Moresi, V., and Saccone, V. (2023). Histone Deacetylases: Molecular Mechanisms and Therapeutic Implications for Muscular Dystrophies. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24054306"},{"key":"ref_473","doi-asserted-by":"crossref","first-page":"e315","DOI":"10.1002\/mco2.315","article-title":"Applications of multi-omics analysis in human diseases","volume":"4","author":"Chen","year":"2023","journal-title":"MedComm"},{"key":"ref_474","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1042\/EBC20180003","article-title":"Systems biology primer: The basic methods and approaches","volume":"62","author":"Tavassoly","year":"2018","journal-title":"Essays Biochem."},{"key":"ref_475","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1002\/wsbm.1184","article-title":"Systems biology of skeletal muscle: Fiber type as an organizing principle","volume":"4","author":"Greising","year":"2012","journal-title":"Wiley Interdiscip. Rev. Syst. Biol. Med."},{"key":"ref_476","doi-asserted-by":"crossref","unstructured":"Heier, C.R., Zhang, A., Nguyen, N.Y., Tully, C.B., Panigrahi, A., Gordish-Dressman, H., Pandey, S.N., Guglieri, M., Ryan, M.M., and Clemens, P.R. (2020). Multi-Omics Identifies Circulating miRNA and Protein Biomarkers for Facioscapulohumeral Dystrophy. J. Pers. Med., 10.","DOI":"10.3390\/jpm10040236"},{"key":"ref_477","doi-asserted-by":"crossref","first-page":"101576","DOI":"10.1016\/j.arr.2022.101576","article-title":"Multi-omics research in sarcopenia: Current progress and future prospects","volume":"76","author":"Liu","year":"2022","journal-title":"Ageing Res. Rev."},{"key":"ref_478","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13395-022-00311-x","article-title":"Multi-omics analysis of sarcospan overexpression in mdx skeletal muscle reveals compensatory remodeling of cytoskeleton-matrix interactions that promote mechanotransduction pathways","volume":"13","author":"McCourt","year":"2023","journal-title":"Skelet. Muscle"},{"key":"ref_479","doi-asserted-by":"crossref","first-page":"e81843","DOI":"10.7554\/eLife.81843","article-title":"Molecular characterization of the intact mouse muscle spindle using a multi-omics approach","volume":"12","author":"Bornstein","year":"2023","journal-title":"eLife"},{"key":"ref_480","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1080\/03008207.2020.1791103","article-title":"Multiomics analysis of the mdx\/mTR mouse model of Duchenne muscular dystrophy","volume":"62","author":"Kharaz","year":"2021","journal-title":"Connect. Tissue Res."},{"key":"ref_481","doi-asserted-by":"crossref","unstructured":"Elasbali, A.M., Al-Soud, W.A., Adnan, M., Alhassan, H.H., Mohammad, T., and Hassan, M.I. (2024). Discovering Promising Biomarkers and Therapeutic Targets for Duchenne Muscular Dystrophy: A Multiomics Meta-Analysis Approach. Mol. Neurobiol.","DOI":"10.1007\/s12035-023-03868-w"},{"key":"ref_482","doi-asserted-by":"crossref","unstructured":"Signorelli, M., Tsonaka, R., Aartsma-Rus, A., and Spitali, P. (2023). Multiomic characterization of disease progression in mice lacking dystrophin. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0283869"},{"key":"ref_483","doi-asserted-by":"crossref","first-page":"1017423","DOI":"10.3389\/fimmu.2022.1017423","article-title":"Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis","volume":"13","author":"Wu","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_484","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/jcsm.12665","article-title":"Myogenesis modelled by human pluripotent stem cells: A multi-omic study of Duchenne myopathy early onset","volume":"12","author":"Mournetas","year":"2021","journal-title":"J. Cachexia Sarcopenia Muscle"},{"key":"ref_485","doi-asserted-by":"crossref","first-page":"e18530","DOI":"10.1016\/j.heliyon.2023.e18530","article-title":"Integrated genomic, proteomic and cognitive assessment in Duchenne Muscular Dystrophy suggest astrocyte centric pathology","volume":"9","author":"Wijekoon","year":"2023","journal-title":"Heliyon"},{"key":"ref_486","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1080\/14789450.2022.2070476","article-title":"An overview of technologies for MS-based proteomics-centric multi-omics","volume":"19","author":"Rajczewski","year":"2022","journal-title":"Expert Rev. Proteom."},{"key":"ref_487","doi-asserted-by":"crossref","unstructured":"Argelaguet, R., Velten, B., Arnol, D., Dietrich, S., Zenz, T., Marioni, J.C., Buettner, F., Huber, W., and Stegle, O. (2018). Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol., 14.","DOI":"10.15252\/msb.20178124"},{"key":"ref_488","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1016\/j.cels.2021.06.006","article-title":"Artificial intelligence for proteomics and biomarker discovery","volume":"12","author":"Mann","year":"2021","journal-title":"Cell Syst."},{"key":"ref_489","doi-asserted-by":"crossref","first-page":"851491","DOI":"10.3389\/fcvm.2022.851491","article-title":"Treating Duchenne Muscular Dystrophy: The Promise of Stem Cells, Artificial Intelligence, and Multi-Omics","volume":"9","author":"Vera","year":"2022","journal-title":"Front Cardiovasc. Med."},{"key":"ref_490","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1021\/acs.jproteome.2c00473","article-title":"Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data","volume":"22","author":"Torun","year":"2023","journal-title":"J. Proteome Res."},{"key":"ref_491","doi-asserted-by":"crossref","unstructured":"Procopio, A., Cesarelli, G., Donisi, L., Merola, A., Amato, F., and Cosentino, C. (2023). Combined mechanistic modeling and machine-learning approaches in systems biology\u2014A systematic literature review. Comput. Methods Programs Biomed., 240.","DOI":"10.1016\/j.cmpb.2023.107681"},{"key":"ref_492","doi-asserted-by":"crossref","first-page":"1288721","DOI":"10.3389\/fneur.2023.1288721","article-title":"DMD deletions underlining mild dystrophinopathies: Literature review highlights phenotype-related mutation clusters and provides insights about genetic mechanisms and prognosis","volume":"14","author":"Fortunato","year":"2024","journal-title":"Front. Neurol."},{"key":"ref_493","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1002\/mus.20697","article-title":"Intrinsic laryngeal muscles are spared from myonecrosis in the mdx mouse model of Duchenne muscular dystrophy","volume":"35","author":"Marques","year":"2007","journal-title":"Muscle Nerve"},{"key":"ref_494","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13395-023-00325-z","article-title":"Biomarkers for Duchenne muscular dystrophy progression: Impact of age in the mdx tongue spared muscle","volume":"13","author":"Lorena","year":"2023","journal-title":"Skelet. Muscle"}],"container-title":["Proteomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-7382\/12\/1\/4\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T13:48:13Z","timestamp":1760104093000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-7382\/12\/1\/4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,16]]},"references-count":494,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,3]]}},"alternative-id":["proteomes12010004"],"URL":"https:\/\/doi.org\/10.3390\/proteomes12010004","relation":{},"ISSN":["2227-7382"],"issn-type":[{"value":"2227-7382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,16]]}}}