DEprot : a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data
Abstract
Abstract In recent years, studies investigating protein–protein interactions on a proteome-wide scale have increased exponentially. These developments were achieved through implementation of new techniques, as well as improvements in mass spectrometry hardware. However, issues specific to this type of technique, such as distinct imputation of random and not-at-random missing proteins, have not been completely addressed. Here, we present DEprot, an R-package providing a comprehensive toolset for end-to-end analysis and visualization of proteomics data. Moreover, we implemented a serial imputation strategy for handling non-random missing values, particularly suitable for protein enrichment techniques and knockout conditions.
Fields of Study & Subjects
Advanced Proteomics Techniques and Applications
Bioinformatics and Genomic Networks
Genomics and Phylogenetic Studies
Publication details
- Journal / source
- NAR Genomics and Bioinformatics
- Volume
- 8
- Issue
- 1
- Pages
- lqag015–lqag015
- Publication date
- 6 January 2026
- Language
- EN