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2020-12-07Zeitschriftenartikel DOI: 10.7554/eLife.58783
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
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.
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DOI
10.7554/eLife.58783
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https://doi.org/10.7554/eLife.58783
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<a href="https://doi.org/10.7554/eLife.58783">https://doi.org/10.7554/eLife.58783</a>