Protocol for generating protein profiles and distance-based network analysis of murine tissue slices
Summary: We introduce a protocol for spatial proteomics using thin cryotome sections of mouse skeletal muscle tissue. We describe steps for preparing muscle sections and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to generate spatial protein profiles along the longitudinal ske...
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007433 |
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| author | Luisa Schmidt Philipp Antczak Marcus Krüger |
| author_facet | Luisa Schmidt Philipp Antczak Marcus Krüger |
| author_sort | Luisa Schmidt |
| collection | DOAJ |
| description | Summary: We introduce a protocol for spatial proteomics using thin cryotome sections of mouse skeletal muscle tissue. We describe steps for preparing muscle sections and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to generate spatial protein profiles along the longitudinal skeletal muscle axis. We detail procedures for scanning longitudinal protein profiles and replacing missing data using a sliding window approach. This protocol has potential for applications in spatial proteomics to other tissues with asymmetric patterns such as the brain and heart tissue.For complete details on the use and execution of this protocol, please refer to Schmidt et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-4a510b6d730e459a93aefde8e653d08f |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-4a510b6d730e459a93aefde8e653d08f2025-01-18T05:05:14ZengElsevierSTAR Protocols2666-16672025-03-0161103578Protocol for generating protein profiles and distance-based network analysis of murine tissue slicesLuisa Schmidt0Philipp Antczak1Marcus Krüger2Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Corresponding authorInstitute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, GermanyInstitute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; Corresponding authorSummary: We introduce a protocol for spatial proteomics using thin cryotome sections of mouse skeletal muscle tissue. We describe steps for preparing muscle sections and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to generate spatial protein profiles along the longitudinal skeletal muscle axis. We detail procedures for scanning longitudinal protein profiles and replacing missing data using a sliding window approach. This protocol has potential for applications in spatial proteomics to other tissues with asymmetric patterns such as the brain and heart tissue.For complete details on the use and execution of this protocol, please refer to Schmidt et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166724007433BioinformaticsCell BiologyProtein Biochemistry |
| spellingShingle | Luisa Schmidt Philipp Antczak Marcus Krüger Protocol for generating protein profiles and distance-based network analysis of murine tissue slices STAR Protocols Bioinformatics Cell Biology Protein Biochemistry |
| title | Protocol for generating protein profiles and distance-based network analysis of murine tissue slices |
| title_full | Protocol for generating protein profiles and distance-based network analysis of murine tissue slices |
| title_fullStr | Protocol for generating protein profiles and distance-based network analysis of murine tissue slices |
| title_full_unstemmed | Protocol for generating protein profiles and distance-based network analysis of murine tissue slices |
| title_short | Protocol for generating protein profiles and distance-based network analysis of murine tissue slices |
| title_sort | protocol for generating protein profiles and distance based network analysis of murine tissue slices |
| topic | Bioinformatics Cell Biology Protein Biochemistry |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007433 |
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