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Pauper M, Hentschel A, Tiburcy M, Beltran S, Ruck T, Schara-Schmidt U, Roos A. Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future. Biomolecules 2025; 15:130. [PMID: 39858524 PMCID: PMC11763865 DOI: 10.3390/biom15010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 12/25/2024] [Accepted: 01/07/2025] [Indexed: 01/27/2025] Open
Abstract
Proteomics accelerates diagnosis and research of muscular diseases by enabling the robust analysis of proteins relevant for the manifestation of neuromuscular diseases in the following aspects: (i) evaluation of the effect of genetic variants on the corresponding protein, (ii) prediction of the underlying genetic defect based on the proteomic signature of muscle biopsies, (iii) analysis of pathophysiologies underlying different entities of muscular diseases, key for the definition of new intervention concepts, and (iv) patient stratification according to biochemical fingerprints as well as (v) monitoring the success of therapeutic interventions. This review presents-also through exemplary case studies-the various advantages of mass proteomics in the investigation of genetic muscle diseases, discusses technical limitations, and provides an outlook on possible future application concepts. Hence, proteomics is an excellent large-scale analytical tool for the diagnostic workup of (hereditary) muscle diseases and warrants systematic profiling of underlying pathophysiological processes. The steady development may allow to overcome existing limitations including a quenched dynamic range and quantification of different protein isoforms. Future directions may include targeted proteomics in diagnostic settings using not only muscle biopsies but also liquid biopsies to address the need for minimally invasive procedures.
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Affiliation(s)
- Marc Pauper
- Centro Nacional de Análisis Genómico (CNAG), Baldiri Reixac 4, 08028 Barcelona, Spain; (M.P.); (S.B.)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany;
| | - Malte Tiburcy
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Georg August University, 37075 Göttingen, Germany;
- ZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG), Baldiri Reixac 4, 08028 Barcelona, Spain; (M.P.); (S.B.)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Tobias Ruck
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany;
- Department of Neurology, BG-University Hospital Bergmannsheil, Ruhr University Bochum, 44789 Bochum, Germany
- Heimer Institute for Muscle Research, BG-University Hospital Bergmannsheil, 44789 Bochum, Germany
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, University Duisburg-Essen, 45147 Essen, Germany;
| | - Andreas Roos
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany;
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, University Duisburg-Essen, 45147 Essen, Germany;
- Brain and Mind Research Institute, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
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DeRosa C, Weaver SD, Wang CW, Schuster-Little N, Whelan RJ. Simultaneous N-Deglycosylation and Digestion of Complex Samples on S-Traps Enables Efficient Glycosite Hypothesis Generation. ACS OMEGA 2023; 8:4410-4418. [PMID: 36743002 PMCID: PMC9893465 DOI: 10.1021/acsomega.2c08071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
N-linked glycosylation is an important post-translational modification that is difficult to identify and quantify in traditional bottom-up proteomics experiments. Enzymatic deglycosylation of proteins by peptide:N-glycosidase F (PNGase F) prior to digestion and subsequent mass spectrometry analysis has been shown to improve coverage of various N-linked glycopeptides, but the inclusion of this step may add up to a day to an already lengthy sample preparation process. An efficient way to integrate deglycosylation with bottom-up proteomics would be a valuable contribution to the glycoproteomics field. Here, we demonstrate a proteomics workflow in which deglycosylation and proteolytic digestion of samples occur simultaneously using suspension trapping (S-Trap). This approach adds no time to standard digestion protocols. Applying this sample preparation strategy to a human serum sample, we demonstrate improved identification of potential N-glycosylated peptides in deglycosylated samples compared with non-deglycosylated samples, identifying 156 unique peptides that contain the N-glycosylation motif (asparagine-X-serine/threonine), the deamidation modification characteristic of PNGase F, and an increase in peptide intensity over a control sample. We expect that this rapid sample preparation strategy will assist in the identification and quantification of both known and potential glycoproteins. Data are available via ProteomeXchange with the identifier PXD037921.
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Affiliation(s)
- Christine
M. DeRosa
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Simon D. Weaver
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
- Integrated
Biomedical Sciences Graduate Program, University
of Notre Dame, Notre Dame, Indiana 46656, United States
| | - Chien-Wei Wang
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | | | - Rebecca J. Whelan
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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