Preprocessing and Analysis of LC-MS-Based Proteomic Data

Tsung-Heng Tsai; Minkun Wang; Habtom W Ressom

doi:10.1007/978-1-4939-3106-4_3

Preprocessing and Analysis of LC-MS-Based Proteomic Data

Methods Mol Biol. 2016:1362:63-76. doi: 10.1007/978-1-4939-3106-4_3.

Authors

Tsung-Heng Tsai^{1

2}, Minkun Wang^{3

4}, Habtom W Ressom³

Affiliations

¹ Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA. thtsai@vt.edu.
² Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA. thtsai@vt.edu.
³ Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.
⁴ Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA.

Abstract

Liquid chromatography coupled with mass spectrometry (LC-MS) has been widely used for profiling protein expression levels. This chapter is focused on LC-MS data preprocessing, which is a crucial step in the analysis of LC-MS based proteomics. We provide a high-level overview, highlight associated challenges, and present a step-by-step example for analysis of data from LC-MS based untargeted proteomic study. Furthermore, key procedures and relevant issues with the subsequent analysis by multiple reaction monitoring (MRM) are discussed.

Keywords: Data preprocessing; Label-free; Liquid chromatography-mass spectrometry (LC-MS); Multiple reaction monitoring (MRM ); Proteomics.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Chromatography, Liquid / methods
Data Interpretation, Statistical
Electronic Data Processing
Mass Spectrometry / methods
Proteome*
Proteomics / methods*

Substances

Proteome

Abstract

Publication types

MeSH terms

Substances

Grants and funding