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2020-12-07Zeitschriftenartikel DOI: 10.7554/eLife.58783
FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data
dc.contributor.authorSchlaffner, Christoph N.
dc.contributor.authorKahnert, Konstantin
dc.contributor.authorMuntel, Jan
dc.contributor.authorChauhan, Ruchi
dc.contributor.authorRenard, Bernhard Y.
dc.contributor.authorSteen, Judith A.
dc.contributor.authorSteen, Hanno
dc.date.accessioned2021-02-09T11:30:28Z
dc.date.available2021-02-09T11:30:28Z
dc.date.issued2020-12-07none
dc.identifier.other10.7554/eLife.58783
dc.identifier.urihttp://edoc.rki.de/176904/7761
dc.description.abstractImprovements 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.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleFLEXIQuant-LF to quantify protein modification extent in label-free proteomics datanone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/7761-3
dc.identifier.doihttps://doi.org/10.7554/eLife.58783
dc.identifier.doihttp://dx.doi.org/10.25646/7983
dc.type.versionpublishedVersionnone
local.edoc.container-titleBiochemistry and Chemical Biologynone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://elifesciences.org/articles/58783none
local.edoc.container-publisher-nameeLifenone
local.edoc.container-issue9none
local.edoc.container-reportyear2020none
local.edoc.container-firstpage1none
local.edoc.container-lastpage21none
local.edoc.rki-departmentMethodenentwicklung und Forschungsinfrastrukturnone
dc.description.versionPeer Reviewednone

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