Seminar: Deep proteome and secretome analysis of skeletal muscle

August Krogh Club triple Seminar

14:00-14:40: Professor Stefano Schiaffino: "Muscle fiber types: from candidate transcript/protein analyses to global omics approaches"
14:40-15:20: Assistant Professor Marta Murgia: “Exploring skeletal muscle plasticity and age-related changes by single fiber proteomics” 
15:20-16:00: Associate Professor Atul Shahaji Deshmukh: “Deep proteome and secretome analysis of skeletal muscle”
16:00-17:00: Post seminar servings and socializing.

Deep proteome and secretome analysis of skeletal muscle proteomics

v/ Associate Professor Atul Shahaji Deshmukh, Clinical Proteomics Group, NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.


Proteomics analysis of skeletal muscle is challenging because of highly abundant contractile proteins that interefere with detection of low abundant proteins. Using-state-of the art MS workflows, we measured deep muscle proteomes and secretome. We applied to these workflows to monitor exercise-induced remodeling of skeletal muscle as well as to investigate metabolic rearrangements in pathological conditions such as diabetes and obesity. Our studies lead to discovery of hundreds of novel proteins which were not associated with exercise or diabetes and suggest starting points for exploring their role in muscle metabolism.


Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M. Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors. Molecular and Cellular Proteomics. 2015 Apr;14(4):841-53.

Deshmukh AS, Cox J, Jensen LJ, Meissner F, Mann M. Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow, Journal of Proteome Research, 2015 Nov 6;14(11):4885-95.

Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS. Proteomics Analysis of Skeletal Muscle from Leptin-Deficient ob/ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition. Proteomics, 2018 Mar;18(5-6)..

Research profile

Atul Deshmukh did his PhD in medical sciences from Karolinska Institute (Sweden) with the primary focus on insulin and exercise-induced signaling pathways in skeletal muscle. He was awarded FEBS fellowship to join Prof. Matthias Mann’s laboratory at Max-Planck Institute for Biochemistry, Munich for his postdoctoral studies. During his post-doctoral studies, he developed methods to analyze deep muscle proteome and secretomes.

Dr. Atul Deshmukh is currently an Associate Professor in the Clinical Proteomics group of Matthias Mann at NNF Center for Protein Research. Building on his post-doctoral research, he continued his work of muscle proteomics in the context of exercise biology and insulin resistance.

Additionally, he is project leader for pharma collaborations involving secretome and peptidome analysis of primary human brown cells (Novo Nordisk AS) and electrically-stimulated primary human skeletal muscle cells (Janssen Pharmaceuticals). .


Auditorium 1, August Krogh Building, Universitetsparken 13, DK-2100 Copenhagen


Participation is free, but please register here.

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