Benchmarking differential expression, imputation and quantification methods for 
proteomics data

Lin, Miao-Hsia; Wu, Pei-Shan; Wong, Tzu-Hsuan; Lin, I-Ying; Lin, Johnathan; Cox, Jürgen; Yu, Sung-Huan

doi:10.1093/bib/bbac138

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Benchmarking differential expression, imputation and quantification methods for proteomics data

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Cox, Jürgen
Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society;

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Citation

Lin, M.-H., Wu, P.-S., Wong, T.-H., Lin, I.-Y., Lin, J., Cox, J., et al. (2022). Benchmarking differential expression, imputation and quantification methods for proteomics data. Briefings in Bioinformatics, 23(3): bbac138. doi:10.1093/bib/bbac138.

Cite as: https://hdl.handle.net/21.11116/0000-000A-6740-A

Abstract

Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools for protein quantification, imputation and differential expression (DE) analysis were generated in the past decade and the search for optimal tools is still going on. Moreover, due to the rapid development of RNA sequencing (RNA-seq) technology, a vast number of DE analysis methods were created for that purpose. The applicability of these newly developed RNA-seq-oriented tools to proteomics data remains in doubt. In order to benchmark these analysis methods, a proteomics dataset consisting of proteins derived from humans, yeast and drosophila, in defined ratios, was generated in this study. Based on this dataset, DE analysis tools, including microarray-and RNA-seq-based ones, imputation algorithms and protein quantification methods were compared and benchmarked. Furthermore, applying these approaches to two public datasets showed that RNA-seq-based DE tools achieved higher accuracy (ACC) in identifying DEPs. This study provides useful guidelines for analyzing quantitative proteomics datasets. All the methods used in this study were integrated into the Perseus software, version 2.0.3.0, which is available at https://www.maxquant.org/perseus.