title: Preprocessing and Analysis of LC-MS-Based Proteomic Data.
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.
authors.affiliation: Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA. thtsai@vt.edu.|Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA. thtsai@vt.edu.
authors.forename: Tsung-Heng
authors.initials: TH
authors.lastname: Tsai
authors.affiliation: Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.|Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA.
authors.forename: Minkun
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20057, USA.
authors.forename: Habtom W
authors.initials: HW
authors.lastname: Ressom
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D003627:Data Interpretation, Statistical; D001330:Electronic Data Processing; D013058:Mass Spectrometry / Q000379:methods; D020543:Proteome; D040901:Proteomics / Q000379:methods*
chemical_list: D020543:Proteome
keywords: Data preprocessing; Label-free; Liquid chromatography-mass spectrometry (LC-MS); Multiple reaction monitoring (MRM ); Proteomics