Protocol for generating protein profiles and distance-based network analysis of murine tissue slices

Luisa Schmidt; Philipp Antczak; Marcus Krüger

doi:10.1016/j.xpro.2024.103578

Protocol for generating protein profiles and distance-based network analysis of murine tissue slices

Luisa Schmidt, Philipp Antczak, Marcus Krüger

Research output: Contribution to journal › Article › peer-review

Abstract

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

Original language	English
Article number	103578
Journal	STAR Protocols
Volume	6
Issue number	1
DOIs	https://doi.org/10.1016/j.xpro.2024.103578
State	Published - 21 Mar 2025
Externally published	Yes

Keywords

Bioinformatics
Cell Biology
Protein Biochemistry

Access to Document

10.1016/j.xpro.2024.103578

Cite this

@article{bdea1aa48e6248199737d0e888001611,

title = "Protocol for generating protein profiles and distance-based network analysis of murine tissue slices",

abstract = "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",

keywords = "Bioinformatics, Cell Biology, Protein Biochemistry",

author = "Luisa Schmidt and Philipp Antczak and Marcus Kr{\"u}ger",

note = "Publisher Copyright: {\textcopyright} 2024 The Authors",

year = "2025",

month = mar,

day = "21",

doi = "10.1016/j.xpro.2024.103578",

language = "English",

volume = "6",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "1",

}

TY - JOUR

T1 - Protocol for generating protein profiles and distance-based network analysis of murine tissue slices

AU - Schmidt, Luisa

AU - Antczak, Philipp

AU - Krüger, Marcus

PY - 2025/3/21

Y1 - 2025/3/21

N2 - 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

AB - 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

KW - Bioinformatics

KW - Cell Biology

KW - Protein Biochemistry

UR - http://www.scopus.com/inward/record.url?scp=85215428594&partnerID=8YFLogxK

U2 - 10.1016/j.xpro.2024.103578

DO - 10.1016/j.xpro.2024.103578

M3 - Article

AN - SCOPUS:85215428594

SN - 2666-1667

VL - 6

JO - STAR Protocols

JF - STAR Protocols

IS - 1

M1 - 103578

ER -

Protocol for generating protein profiles and distance-based network analysis of murine tissue slices

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this