Label-free proteome quantification and evaluation

作者全名："Fu, Jianbo; Yang, Qingxia; Luo, Yongchao; Zhang, Song; Tang, Jing; Zhang, Ying; Zhang, Hongning; Xu, Hanxiang; Zhu, Feng"

作者地址："[Fu, Jianbo; Luo, Yongchao; Zhang, Song; Zhang, Ying; Zhang, Hongning; Xu, Hanxiang; Zhu, Feng] Zhejiang Univ, Coll Pharmaceut Sci, Hangzhou 310050, Peoples R China; [Yang, Qingxia] Nanjing Univ Posts & Telecommun, Sch Geog & Biol Informat, Nanjing, Peoples R China; [Tang, Jing] Chongqing Med Univ, Dept Bioinformat, Chongqing, Peoples R China"

通信作者："Zhu, F (通讯作者)，Zhejiang Univ, Coll Pharmaceut Sci, Hangzhou 310050, Peoples R China."

来源：BRIEFINGS IN BIOINFORMATICS

ESI学科分类：COMPUTER SCIENCE

WOS号：WOS:000893227200001

JCR分区：Q1

影响因子：9.5

年份：2023

卷号：　

期号：　

开始页：　

结束页：　

文献类型：Article; Early Access

关键词：label-free quantification; proteomics; comprehensive evaluation; well-performing chains; R package

摘要："The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on > 3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.[GRAPHICS}."

基金机构："National Natural Science Foundation of China [81872798, U1909208]; Natural Science Foundation of Zhejiang Province [LR21H300001]; Natural Science Foundation of Jiangsu Province [BK20210597]; Leading Talent of the Ten Thousand Plan' - National High-Level Talents Special Support Plan of China; Fundamental Research Fund of Central University [2018QNA7023]; Key R&D Program of Zhejiang Province [2020C03010]; National Key R&D Program of China Synthetic Biology Research [2019YFA0905900]; ""Double Top-Class"" University [181201*194232101]; Space Exploration Breeding Grant of Qian Xuesen Lab [TKTSPY-2020-04-03]; Scientific Research Grant of Ningbo University [215-432000282]; Ningbo Top Talent Proj [215-432094250]; Shenzhen Municipal Government grant [2019156, JCYJ20170413113448742, 201901]; Department of Science & Technology of Guangdong Province [2017B030314083]; Westlake Laboratory (Westlake Laboratory of Life Sciences and Biomedicine); Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare; Alibaba Cloud; InformationTechnology Center of Zhejiang University"

基金资助正文："Funded by the National Natural Science Foundation of China (81872798 & U1909208); Natural Science Foundation of Zhe-jiang Province (LR21H300001); Natural Science Foundation of Jiangsu Province (BK20210597); Leading Talent of the Ten Thousand Plan' - National High-Level Talents Special SupportPlan of China; Fundamental Research Fund of Central University (2018QNA7023); Key R&D Program of Zhejiang Province(2020C03010); National Key R&D Program of China Synthetic Biology Research (2019YFA0905900); ""Double Top-Class"" Uni-versity (181201*194232101); Space Exploration Breeding Grant of Qian Xuesen Lab (TKTSPY-2020-04-03); Scientific Research Grant of Ningbo University (215-432000282); Ningbo Top Talent Proj (215-432094250); Shenzhen Municipal Government grant(NO.2019156, JCYJ20170413113448742, NO.201901); Department of Science & Technology of Guangdong Province (2017B030314083);Westlake Laboratory (Westlake Laboratory of Life Sciences and Biomedicine), Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba Cloud, InformationTechnology Center of Zhejiang University."