Comprehensive Evaluation and Optimization of the Data-Dependent LC-MS/MS Workflow for Deep Proteome Profiling

Tang, Min1,2; Huang, Peiwu3,4; Wu, Lize5,6; Zhou, Piyu7; Gong, Pengyun1,2; Liu, Xiang1,2; Wei, Qiushi1,2; Hou, Xinhang1,2; Hu, Hongke1,2; Zhang, Ao1,2; Shen, Chengpin8; Gao, Weina3,4; Tian, Ruijun3,4; Liu, Chao1,2

2023-05-10

10.1021/acs.analchem.3c00338

ANALYTICAL CHEMISTRY   影响因子和分区

0003-2700

1520-6882

Data-dependentliquid chromatography-tandem massspectrometry(LC-MS/MS) is widely used in proteomic analyses. A well-performedLC-MS/MS workflow, which involves multiple procedures and interdependentmetrics, is a prerequisite for deep proteome profiling. Researchershave previously evaluated LC-MS/MS performance mainly basedon the number of identified peptides and proteins. However, this isnot a comprehensive approach. This motivates us to develop MSRefine,which aims to evaluate and optimize the performance of the LC-MS/MSworkflow for data-dependent acquisition (DDA) proteomics. It extracts 47 kinds of metrics, scores the metrics, and reports visual results,assisting users in evaluating the workflow, locating problems, andproviding optimizing strategies. In this study, we compared and analyzedmultiple pairs of datasets spanning different samples, methods, andinstruments and demonstrated that the comprehensive visual metricsand scores in MSRefine enable us to evaluate the performance of thevarious experiments and provide optimal strategies for the identificationof more peptides and proteins.

SCI ; EI

英语

NI论文

通讯

National Key R&D Program of China["2021YFA1301602","2021YFA1301603"] ; National Natural Science Foundation of China[32171442]

Chemistry

Chemistry, Analytical

WOS:001010178800001

AMER CHEMICAL SOC

20232314180995

Liquid chromatography ; Mass spectrometry ; Molecular biology

Biology:461.9 ; Chemistry:801

CHEMISTRY

Web of Science

1.Beihang Univ, Sch Biol Sci & Med Engn, Beijing 100191, Peoples R China
2.Beihang Univ, Sch Engn Med, Beijing 100191, Peoples R China
3.Southern Univ Sci & Technol, Dept Chem, Shenzhen 518055, Peoples R China
4.Southern Univ Sci & Technol, Res Ctr Chem Biol & Om Anal, Shenzhen 518055, Peoples R China
5.Zhejiang Univ, Inst Immunol, Sch Med, Hangzhou 310058, Zhejiang, Peoples R China
6.Zhejiang Univ, Sir Run Run Shaw Hosp, Sch Med, Dept Rheumatol, Hangzhou 310058, Zhejiang, Peoples R China
7.Shandong Univ Technol, Sch Comp Sci & Technol, Zibo 266590, Peoples R China
8.Shanghai Omicsolut Co Ltd, Shanghai 201199, Peoples R China

Tang, Min,Huang, Peiwu,Wu, Lize,et al. Comprehensive Evaluation and Optimization of the Data-Dependent LC-MS/MS Workflow for Deep Proteome Profiling[J]. ANALYTICAL CHEMISTRY,2023,95(20):7897-7905.

Tang, Min.,Huang, Peiwu.,Wu, Lize.,Zhou, Piyu.,Gong, Pengyun.,...&Liu, Chao.(2023).Comprehensive Evaluation and Optimization of the Data-Dependent LC-MS/MS Workflow for Deep Proteome Profiling.ANALYTICAL CHEMISTRY,95(20),7897-7905.

Tang, Min,et al."Comprehensive Evaluation and Optimization of the Data-Dependent LC-MS/MS Workflow for Deep Proteome Profiling".ANALYTICAL CHEMISTRY 95.20(2023):7897-7905.