Document Type

Article

Publication Date

8-1-2021

Publication Title

Mol Syst Biol

Keywords

JMG

JAX Source

Mol Syst Biol 2021; 17(8):e10240

Volume

17

Issue

8

First Page

10240

Last Page

10240

ISSN

1744-4292

PMID

34432947

DOI

https://doi.org/10.15252/msb.202110240

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 on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.

Comments

This is an open access article under the terms of the Creative Commons Attribution License.

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