Work

DEprot : a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data

Year: 2026

Type: article

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.

Source: NAR Genomics and Bioinformatics

DOI: 10.1093/nargab/lqag015

Authors: Nils Eickhoff, Liesbeth Hoekman, Onno Bleijerveld, Andries M Bergman, Wilbert Zwart, Sebastian Gregoricchio

Institutions: The Netherlands Cancer Institute, Oncode Institute, Amsterdam University Medical Centers, Eindhoven University of Technology

Language: English

Topic: Advanced Proteomics Techniques and Applications

Subfield: Spectroscopy

Field: Chemistry

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $2,766

Funders: Ministerie van Volksgezondheid, Welzijn en Sport, KWF Kankerbestrijding, Oncode Institute