Article (Scientific journals)
Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.
Čuklina, Jelena; Lee, Chloe H.; Williams, Evan et al.
2021In Molecular Systems Biology, 17 (8), p. 10240
Peer Reviewed verified by ORBi
 

Files


Full Text
00_FINAL_PUBLICATION_VERSION.pdf
Publisher postprint (2.66 MB)
Download

All documents in ORBilu are protected by a user license.

Send to



Details



Keywords :
batch effects; data analysis; large-scale proteomics; normalization; quantitative proteomics
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Čuklina, Jelena
Lee, Chloe H.
Williams, Evan  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Gene Expression and Metabolism
Sajic, Tatjana
Collins, Ben C.
Rodríguez Martínez, María
Sharma, Varun S.
Wendt, Fabian
Goetze, Sandra
Keele, Gregory R.
Wollscheid, Bernd
Aebersold, Ruedi
Pedrioli, Patrick G. A.
More authors (3 more) Less
External co-authors :
yes
Language :
English
Title :
Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.
Publication date :
2021
Journal title :
Molecular Systems Biology
ISSN :
1744-4292
Publisher :
Wiley-Blackwell, United States
Volume :
17
Issue :
8
Pages :
e10240
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
© 2021 The Authors. Published under the terms of the CC BY 4.0 license.
Available on ORBilu :
since 15 September 2021

Statistics


Number of views
68 (1 by Unilu)
Number of downloads
49 (2 by Unilu)

Scopus citations®
 
45
Scopus citations®
without self-citations
43
OpenCitations
 
26
WoS citations
 
37

Bibliography


Similar publications



Contact ORBilu