title: Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation.
abstract: 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.
authors.affiliation: Department of Chemistry and Institutes of Biomedical Sciences Shanghai Medical School, Fudan University, Shanghai, P. R. China.
authors.forename: Xuefei
authors.initials: X
authors.lastname: Yin
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Liu
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.forename: Guoquan
authors.initials: G
authors.lastname: Yan
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.forename: Haojie
authors.initials: H
authors.lastname: Lu
authors.forename: Huali
authors.initials: H
authors.lastname: Shen
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Yang
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D060066:Protein Interaction Maps; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D020543:Proteome
keywords: 1D LC-MS/MS; High throughput; Rapid quantification; Technology