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Rapid and sensitive profiling and quantification of the human cell line proteome by LC‐MS/MS without prefractionation
Author(s) -
Yin Xuefei,
Liu Xiaohui,
Zhang Yang,
Yan Guoquan,
Wang Fang,
Lu Haojie,
Shen Huali,
Yang Pengyuan
Publication year - 2014
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201300510
Subject(s) - proteome , proteomics , profiling (computer programming) , chromatography , computational biology , chemistry , biology , computer science , biochemistry , gene , operating system
In this paper, we demonstrate a rapid and reproducible 1D LC‐MS/MS workflow for fast quantitative proteomic research. We have optimized the LC‐MS/MS conditions, including digestion and gradient conditions, sample loading amount, and MS parameter settings. As a result, we were able to obtain twice as many protein identifications compared with the LC‐MS/MS conditions before optimization. More than 4500 protein groups and 50 000 peptides were identified in less than 8 h without any fractionation. This 1D workflow was then applied to the analysis of the MLN4924 treated/untreated human umbilical vein endothelial cell (HUVEC) samples with label‐free quantification. In these experiments, a total of 179 proteins showed a statistically significant expression change after the MLN4924 treatment. Functional analysis showed that these proteins are associated with cell death and survival; gene expression; cell cycle; and DNA replication, recombination, and repair.