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Embryonic Stem Cell Protocols
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SYSNO ASEP 0561137 Document Type M - Monograph Chapter R&D Document Type Monograph Chapter Title Proteomic Analysis of Human Neural Stem Cell Differentiation by SWATH-MS Author(s) Tylečková, Jiřina (UZFG-Y)
Červenka, Jakub (UZFG-Y) ORCID
Poliakh, Ievgeniia (UZFG-Y)
Novák, Jaromír (UZFG-Y)
Vodičková Kepková, Kateřina (UZFG-Y) ORCID
Kupcová Skalníková, Helena (UZFG-Y) RID, ORCID
Vodička, Petr (UZFG-Y) ORCIDSource Title Embryonic Stem Cell Protocols. - New York : Springer Link, 2022 / Turksen Kursad - ISBN 978-1-0716-2436-4 Pages s. 335-360 Number of pages 26 s. Number of copy 500 Number of pages 363 Publication form Print - P Language eng - English Country US - United States Keywords proteomics ; data independent acquisition ; SWATH-MS Subject RIV EB - Genetics ; Molecular Biology OECD category Neurosciences (including psychophysiology R&D Projects LTC18079 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GA19-01747S GA ČR - Czech Science Foundation (CSF) Institutional support UZFG-Y - RVO:67985904 EID SCOPUS 85135282185 DOI 10.1007/7651_2022_462 Annotation The unique properties of stem cells to self-renew and differentiate hold great promise in disease modelling and regenerative medicine. However, more information about basic stem cell biology and thorough characterization of available stem cell lines is needed. This is especially essential to ensure safety before any possible clinical use of stem cells or partially committed cell lines. As proteins are the key effector molecules in the cell, the proteomic characterization of cell lines, cell compartments or cell secretome and microenvironment is highly beneficial to answer above mentioned questions. Nowadays, method of choice for large-scale discovery-based proteomic analysis is mass spectrometry (MS) with data-independent acquisition (DIA). DIA is a robust, highly reproducible, high-throughput quantitative MS approach that enables relative quantification of thousands of proteins in one sample. In the current protocol, we describe a specific variant of DIA known as SWATH-MS for characterization of neural stem cell differentiation. The protocol covers the whole process from cell culture, sample preparation for MS analysis, the SWATH-MS data acquisition on TTOF 5600, the complete SWATH-MS data processing and quality control using Skyline software and the basic statistical analysis in R and MSstats package. The protocol for SWATH-MS data acquisition and analysis can be easily adapted to other samples amenable to MS-based proteomics. Workplace Institute of Animal Physiology and Genetics Contact Jana Zásmětová, knihovna@iapg.cas.cz, Tel.: 315 639 554 Year of Publishing 2023 Electronic address https://link.springer.com/protocol/10.1007/7651_2022_462
Number of the records: 1