Proteomics. 2014 Sep;14(17):2008-16. doi: 10.1002/pmic.201300510. Epub 2014 Aug 13.

Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation.

Proteomics

Xuefei Yin, Xiaohui Liu, Yang Zhang, Guoquan Yan, Fang Wang, Haojie Lu, Huali Shen, Pengyuan Yang

PMID: 25044409 DOI: 10.1002/pmic.201300510

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.

© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Keywords: 1D LC-MS/MS; High throughput; Rapid quantification; Technology

Substances

• Proteome

MeSH terms

• Chromatography, Liquid / methods
• Human Umbilical Vein Endothelial Cells
• Humans
• Protein Interaction Maps
• Proteome / analysis
• Proteome / chemistry
• Proteomics / methods
• Tandem Mass Spectrometry / methods

Publication Types

• Journal Article
• Research Support, Non-U.S. Gov't