A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples

Rune Matthiesen, Manuel S. Rodriguez, Ana Sofia Carvalho

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Mass spectrometry data on ubiquitin and ubiquitin-like modifiers are becoming increasingly more accessible, and the coverage progressively deepen as methodologies mature. This type of mass spectrometry data is linked to specific data analysis pipelines for ubiquitin. This chapter describes a computational tool to facilitate analysis of mass spectrometry data obtained on ubiquitin-enriched samples. For example, the analysis of ubiquitin branch site statistics and functional enrichment analysis against ubiquitin proteasome system protein sets are completed with a few functional calls. We foresee that the proposed computational methodology can aid in proximity drug design by, for example, elucidating the expression of E3 ligases and other factors related to the ubiquitin proteasome system.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press
Number of pages10
Publication statusPublished - 2023

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Mass spectrometry
  • Proteolysis targeting chimera
  • Proximity drugs
  • R programming language
  • Ubiquitin branch statistics
  • Ubiquitin enrichment
  • Ubiquitin proteasome system


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