Comparative evaluation of label-free quantification strategies

doi:10.1016/j.jprot.2020.103669

	Comparative evaluation of label-free quantification strategies
	Zhao, Lei 1; Cong, Xiaoji 2,3; Zhai, Linhui 2; Hu, Hao 2; Xu, Jun-Yu 2; Zhao, Wensi 2,3; Zhu, Mengdi 2,3; Tan, Minjia 2,3; Ye, Bang-Ce 1
刊名	JOURNAL OF PROTEOMICS
	2020-03-20
卷号	215 页码:8
关键词	Label-free quantification Proteomics Precision Accuracy
ISSN号	1874-3919
DOI	10.1016/j.jprot.2020.103669
通讯作者	Tan, Minjia(mjtan@simm.ac.cn) ; Ye, Bang-Ce(bcye@ecust.edu.cn)
英文摘要	The selection of a data processing method for use in mass spectrometry-based label-free proteome quantification contributes significantly to its accuracy and precision. In this study, we comprehensively evaluated 7 commonly-used label-free quantification methods (MaxQuant-Spectrum count, MaxQuant-iBAQ, MaxQuant-LFQ, MaxQuant-LFAQ, Proteome Discoverer, MetaMorpheus, TPP-StPeter) with a focus on missing values, precision, accuracy, selectivity, and reproducibility of low abundance protein quantification in both single shot and fractionation. Our results showed that among the tested strategies, MaxQuant in MaxLFQ mode outperformed other strategies in terms of accuracy and precision in both whole proteome and low abundance proteome quantification, whereas the Proteome Discoverer (PD) strategy using SEQUEST as a search engine performed better in terms of quantifiable low abundance proteome coverage. We subsequently applied the PD and MaxLFQ strategies in a blood proteomic dataset and found that many FDA-approved tumor prognostic biomarkers could be identified as well as quantified using the PD strategy, indicating the potential advantage of PD in label-free quantification studies. These results provide a reference for method choice in label-free quantification data analysis. Significance: Mass spectrometry-based label-free quantification methods play an important role in label-free proteome data analysis. In this study, we evaluated 7 commonly-used label-free quantification methods with respect to the following aspects: missing values, precision, accuracy, selectivity, and reproducibility for low abundance protein quantification. The results showed that, among the strategies evaluated, the PD strategy with SEQUEST as a search engine performed better in terms of low abundance protein coverage. This study provides a reference for method choice in label-free quantification data analysis.
资助项目	Special Project on Precision Medicine under the National Key RD Program[2017YFC0906600] ; National Natural Science Foundation of China[31730004] ; National Natural Science Foundation of China[21575089] ; National Natural Science Foundation of China[31670066] ; National Natural Science Foundation of China[91753203] ; Natural Science Foundation of China for Innovation Research Group[81821005]
WOS关键词	POLYMERIC IMMUNOGLOBULIN RECEPTOR ; COMPLEX PROTEIN MIXTURES ; MASS-SPECTROMETRY ; PLASMA PROTEOME
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	ELSEVIER
WOS记录号	WOS:000519667800012
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/281120]
专题	中国科学院上海药物研究所
通讯作者	Tan, Minjia; Ye, Bang-Ce
作者单位	1.East China Univ Sci & Technol, Lab Biosyst & Microanal, State Key Lab Bioreactor Engn, Shanghai 200237, Peoples R China 2.Chinese Acad Sci, Chem Prote Ctr, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Zhao, Lei,Cong, Xiaoji,Zhai, Linhui,et al. Comparative evaluation of label-free quantification strategies[J]. JOURNAL OF PROTEOMICS,2020,215:8.
APA	Zhao, Lei.,Cong, Xiaoji.,Zhai, Linhui.,Hu, Hao.,Xu, Jun-Yu.,...&Ye, Bang-Ce.(2020).Comparative evaluation of label-free quantification strategies.JOURNAL OF PROTEOMICS,215,8.
MLA	Zhao, Lei,et al."Comparative evaluation of label-free quantification strategies".JOURNAL OF PROTEOMICS 215(2020):8.