Batch effects correction improves the sensitivity of significance tests in spectral counting-based comparative discovery proteomics

Journal of Proteomics
Josep GregoriJosep Villanueva

Abstract

Shotgun proteomics has become the standard proteomics technique for the large-scale measurement of protein abundances in biological samples. Despite quantitative proteomics has been usually performed using label-based approaches, label-free quantitation offers advantages related to the avoidance of labeling steps, no limitation in the number of samples to be compared, and the gain in protein detection sensitivity. However, since samples are analyzed separately, experimental design becomes critical. The exploration of spectral counting quantitation based on LC-MS presented here gathers experimental evidence of the influence of batch effects on comparative proteomics. The batch effects shown with spiking experiments clearly interfere with the biological signal. In order to minimize the interferences from batch effects, a statistical correction is proposed and implemented. Our results show that batch effects can be attenuated statistically when proper experimental design is used. Furthermore, the batch effect correction implemented leads to a substantial increase in the sensitivity of statistical tests. Finally, the applicability of our batch effects correction is shown on two different biomarker discovery projects involving cance...Continue Reading

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Citations

Jun 2, 2016·Analytical Chemistry·Yu-Jen LiangHsin-Chou Yang
Oct 6, 2016·Nanotoxicology·Géraldine KleinJean Labarre
Feb 25, 2014·Molecular & Cellular Proteomics : MCP·Paul A RudnickStephen E Stein
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May 11, 2019·Journal of Proteome Research·Suruchi AggarwalAmit K Yadav
Aug 26, 2021·Molecular Systems Biology·Jelena ČuklinaPatrick G A Pedrioli

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