Data-Processing Workflow for Relative Quantification from Label-Free and Isobaric Labeling-Based Untargeted Shotgun Proteomics: From Database Search to Differential Expression Analysis

Summary This chapter aims to introduce the principal bases of the commonly used data processing workflow for identification and quantification of proteins, toward the goal of improving relative quantification from untargeted label-free or isobaric labeling workflows for shotgun proteomics. Parameters for database search and considerations for quantification workflows, especially imputation and normalization, will be discussed with examples from literature. As most of these data processing methods are well established or reviewed within the LC-MS proteomics literature, these methods should also be transferred and adapted to proteomics research using CE-MS. While this chapter is targeted toward newcomers to proteomics, some of the points are also raised for experts in the field to consider.