Cargando…

FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Schlaffner, Christoph N, Kahnert, Konstantin, Muntel, Jan, Chauhan, Ruchi, Renard, Bernhard Y, Steen, Judith A, Steen, Hanno
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721442/
https://www.ncbi.nlm.nih.gov/pubmed/33284109
http://dx.doi.org/10.7554/eLife.58783
_version_ 1783620021292892160
author Schlaffner, Christoph N
Kahnert, Konstantin
Muntel, Jan
Chauhan, Ruchi
Renard, Bernhard Y
Steen, Judith A
Steen, Hanno
author_facet Schlaffner, Christoph N
Kahnert, Konstantin
Muntel, Jan
Chauhan, Ruchi
Renard, Bernhard Y
Steen, Judith A
Steen, Hanno
author_sort Schlaffner, Christoph N
collection PubMed
description 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.
format Online
Article
Text
id pubmed-7721442
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher eLife Sciences Publications, Ltd
record_format MEDLINE/PubMed
spelling pubmed-77214422020-12-09 FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data Schlaffner, Christoph N Kahnert, Konstantin Muntel, Jan Chauhan, Ruchi Renard, Bernhard Y Steen, Judith A Steen, Hanno eLife Biochemistry and Chemical Biology 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. eLife Sciences Publications, Ltd 2020-12-07 /pmc/articles/PMC7721442/ /pubmed/33284109 http://dx.doi.org/10.7554/eLife.58783 Text en © 2020, Schlaffner et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Biochemistry and Chemical Biology
Schlaffner, Christoph N
Kahnert, Konstantin
Muntel, Jan
Chauhan, Ruchi
Renard, Bernhard Y
Steen, Judith A
Steen, Hanno
FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title_full FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title_fullStr FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title_full_unstemmed FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title_short FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
title_sort flexiquant-lf to quantify protein modification extent in label-free proteomics data
topic Biochemistry and Chemical Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721442/
https://www.ncbi.nlm.nih.gov/pubmed/33284109
http://dx.doi.org/10.7554/eLife.58783
work_keys_str_mv AT schlaffnerchristophn flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT kahnertkonstantin flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT munteljan flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT chauhanruchi flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT renardbernhardy flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT steenjuditha flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata
AT steenhanno flexiquantlftoquantifyproteinmodificationextentinlabelfreeproteomicsdata