Chinese Journal of Chromatography ›› 2014, Vol. 32 ›› Issue (4): 349-354.DOI: 10.3724/SP.J.1123.2013.10030

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A method using spectrum alignment to improve analysis efficiency of liquid chromatography combined with mass spectrometry

LU Wenyuan1,2, ZHANG Yang2, SHEN Chengpin2, YIN Xuefei2, LIU Xiaohui2, YANG Pengyuan1   

  1. 1. Department of Chemistry, Fudan University, Shanghai 200433, China;
    2. Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
  • Received:2013-10-29 Revised:2013-11-28 Online:2014-04-08 Published:2014-03-28

Abstract:

In the analysis of proteins in human umbilical vein endothelial cells (HUVEC) treated with dimethyl sulfoxide (DMSO) and NEDD8-activating enzyme inhibitor (MLN4924,MLN), the Progenesis LC-MS software (Nonlinear Dynamics Ltd) was applied to liquid chromatography spectrum alignment, while spectrum similarities were figured out among several experiments of the same sample, and also among different samples. After double enzymolysis, the sample was added with digested QconCAT standard proteins. They were separated by HPLC-MS/MS, followed by spectrum alignment and data analysis. This established experiment flow offered a better identification result of more than 8000 proteins, while the original result was about 7000 proteins, ensuring a relatively high identification efficiency. On the basis of relative quantification with spectrum count, the described procedure can analyze the differential expression of proteins induced by DMSO and MLN. The similarities of total ion chromatograms after alignment were also compared. This method was proved to be quick and easy, with the advantages of high throughput and high sensitivity.

Key words: high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), protein analysis, spectrum alignment

CLC Number: