@inbook{1df21fff69074aff805e12ba4fd98294,
title = "A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples",
abstract = "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.",
keywords = "Mass spectrometry, Proteolysis targeting chimera, Proximity drugs, R programming language, Ubiquitin branch statistics, Ubiquitin enrichment, Ubiquitin proteasome system",
author = "Rune Matthiesen and Rodriguez, {Manuel S.} and Carvalho, {Ana Sofia}",
note = "Funding Information: R.M. is supported by Funda{\c c}{\~a}o para a Ci{\^e}ncia e a Tecnologia (CEEC position, 2019–2025 investigator). This article is a result of the projects (iNOVA4Health—UIDB/04462/2020), supported by Lisboa Portugal Regional Operational Programme (Lis-boa, 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). This work is also funded by FEDER funds through the COMPETE 2020 Programme and National Funds through FCT—Portuguese Foundation for Science and Technology under the projects number PTDC/BTM-TEC/30087/2017 and PTDC/BTM-TEC/ 30088/2017. This publication is based upon work from COST Action, CA20113 “PROTEOCURE” supported by COST (European Cooperation in Science and Technology). Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2023",
doi = "10.1007/978-1-0716-2859-1_15",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "205--214",
booktitle = "Methods in Molecular Biology",
address = "United States",
}