FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data.
PTM identification
PTM quantification
biochemistry
chemical biology
computational biology
human
label-free quantification
mass spectrometry
modification stoichiometry
peptide modification
systems biology
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
07 12 2020
07 12 2020
Historique:
received:
11
05
2020
accepted:
23
11
2020
entrez:
7
12
2020
pubmed:
8
12
2020
medline:
2
4
2021
Statut:
epublish
Résumé
Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
Identifiants
pubmed: 33284109
doi: 10.7554/eLife.58783
pii: 58783
pmc: PMC7721442
doi:
pii:
Substances chimiques
Peptides
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIH HHS
ID : S10 OD010700
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI124284
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI099204
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA196703
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM112007
Pays : United States
Organisme : NIGMS NIH HHS
ID : RC4 GM096319
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS066973
Pays : United States
Organisme : NICHD NIH HHS
ID : U54 HD090255
Pays : United States
Organisme : Deutsche Forschungsgemeinschaft
ID : RE3474/2-2
Pays : International
Informations de copyright
© 2020, Schlaffner et al.
Déclaration de conflit d'intérêts
CS, KK, JM, RC, BR, JS, HS No competing interests declared
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