Statistical Methods in Proteomics

Summary Proteomics technologies are rapidly evolving and attracting great attention in the post-genome era. In this chapter, we review two key applications of proteomics techniques: disease biomarker discovery and protein/peptide identification. For each of the applications, we will state the major issues related to statistical modeling and analysis, review related work, discuss their strength and weakness, and point out unsolved problems for future research. Concretely, we organize this chapter as follows: Section 1 briefly introduces mass spectrometry (MS) and tandem MS/MS with a few sample plots show- ing data format. Section 2 focuses on MS data pre-processing. We first