Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.

ABSTRACT: Advancements in mass spectrometry-based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much-needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step-by-step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology

SUBMITTER: Cuklina J 

PROVIDER: S-EPMC8447595 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature