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Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

Sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) has emerged as one of the most popular techniques for label-free proteome quantification in current pharmacoproteomic research. It provides more comprehensive detection and more accurate quantitation of proteins...

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Autores principales: Fu, Jianbo, Tang, Jing, Wang, Yunxia, Cui, Xuejiao, Yang, Qingxia, Hong, Jiajun, Li, Xiaoxu, Li, Shuang, Chen, Yuzong, Xue, Weiwei, Zhu, Feng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028727/
https://www.ncbi.nlm.nih.gov/pubmed/29997509
http://dx.doi.org/10.3389/fphar.2018.00681
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author Fu, Jianbo
Tang, Jing
Wang, Yunxia
Cui, Xuejiao
Yang, Qingxia
Hong, Jiajun
Li, Xiaoxu
Li, Shuang
Chen, Yuzong
Xue, Weiwei
Zhu, Feng
author_facet Fu, Jianbo
Tang, Jing
Wang, Yunxia
Cui, Xuejiao
Yang, Qingxia
Hong, Jiajun
Li, Xiaoxu
Li, Shuang
Chen, Yuzong
Xue, Weiwei
Zhu, Feng
author_sort Fu, Jianbo
collection PubMed
description Sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) has emerged as one of the most popular techniques for label-free proteome quantification in current pharmacoproteomic research. It provides more comprehensive detection and more accurate quantitation of proteins comparing with the traditional techniques. The performance of SWATH-MS is highly susceptible to the selection of processing method. Till now, ≥27 methods (transformation, normalization, and missing-value imputation) are sequentially applied to construct numerous analysis chains for SWATH-MS, but it is still not clear which analysis chain gives the optimal quantification performance. Herein, the performances of 560 analysis chains for quantifying pharmacoproteomic data were comprehensively assessed. Firstly, the most complete set of the publicly available SWATH-MS based pharmacoproteomic data were collected by comprehensive literature review. Secondly, substantial variations among the performances of various analysis chains were observed, and the consistently well-performed analysis chains (CWPACs) across various datasets were for the first time generalized. Finally, the log and power transformations sequentially followed by the total ion current normalization were discovered as one of the best performed analysis chains for the quantification of SWATH-MS based pharmacoproteomic data. In sum, the CWPACs identified here provided important guidance to the quantification of proteomic data and could therefore facilitate the cutting-edge research in any pharmacoproteomic studies requiring SWATH-MS technique.
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spelling pubmed-60287272018-07-11 Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification Fu, Jianbo Tang, Jing Wang, Yunxia Cui, Xuejiao Yang, Qingxia Hong, Jiajun Li, Xiaoxu Li, Shuang Chen, Yuzong Xue, Weiwei Zhu, Feng Front Pharmacol Pharmacology Sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) has emerged as one of the most popular techniques for label-free proteome quantification in current pharmacoproteomic research. It provides more comprehensive detection and more accurate quantitation of proteins comparing with the traditional techniques. The performance of SWATH-MS is highly susceptible to the selection of processing method. Till now, ≥27 methods (transformation, normalization, and missing-value imputation) are sequentially applied to construct numerous analysis chains for SWATH-MS, but it is still not clear which analysis chain gives the optimal quantification performance. Herein, the performances of 560 analysis chains for quantifying pharmacoproteomic data were comprehensively assessed. Firstly, the most complete set of the publicly available SWATH-MS based pharmacoproteomic data were collected by comprehensive literature review. Secondly, substantial variations among the performances of various analysis chains were observed, and the consistently well-performed analysis chains (CWPACs) across various datasets were for the first time generalized. Finally, the log and power transformations sequentially followed by the total ion current normalization were discovered as one of the best performed analysis chains for the quantification of SWATH-MS based pharmacoproteomic data. In sum, the CWPACs identified here provided important guidance to the quantification of proteomic data and could therefore facilitate the cutting-edge research in any pharmacoproteomic studies requiring SWATH-MS technique. Frontiers Media S.A. 2018-06-26 /pmc/articles/PMC6028727/ /pubmed/29997509 http://dx.doi.org/10.3389/fphar.2018.00681 Text en Copyright © 2018 Fu, Tang, Wang, Cui, Yang, Hong, Li, Li, Chen, Xue and Zhu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Pharmacology
Fu, Jianbo
Tang, Jing
Wang, Yunxia
Cui, Xuejiao
Yang, Qingxia
Hong, Jiajun
Li, Xiaoxu
Li, Shuang
Chen, Yuzong
Xue, Weiwei
Zhu, Feng
Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title_full Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title_fullStr Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title_full_unstemmed Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title_short Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
title_sort discovery of the consistently well-performed analysis chain for swath-ms based pharmacoproteomic quantification
topic Pharmacology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028727/
https://www.ncbi.nlm.nih.gov/pubmed/29997509
http://dx.doi.org/10.3389/fphar.2018.00681
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