标杆管理
工作流程
软件
计算机科学
数据挖掘
蛋白质组
蛋白质组学
轨道轨道
定量蛋白质组学
生物信息学
质谱法
数据库
化学
生物
色谱法
基因
业务
营销
程序设计语言
生物化学
作者
Clarisse Gotti,Florence Roux‐Dalvai,Charles Joly-Beauparlant,Loïc Mangnier,Mickaël Leclercq,Arnaud Droit
标识
DOI:10.1021/acs.jproteome.1c00490
摘要
Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1-Sigma) at 8 different concentrations in an E. coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline, and Spectronaut) with or without the use of a DDA spectral library. On the basis of the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.
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