F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, United States; Department of Neurology, Harvard Medical School, Boston, United States
Department of Pathology, Boston Children’s Hospital, Boston, United States; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany; Department of Medical Biotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
Department of Pathology, Boston Children’s Hospital, Boston, United States; Department of Pathology, Harvard Medical School, Boston, United States
Ruchi Chauhan
F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, United States
Bernhard Y Renard
Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany; Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
Judith A Steen
F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, United States; Department of Neurology, Harvard Medical School, Boston, United States
Department of Pathology, Boston Children’s Hospital, Boston, United States; Department of Pathology, Harvard Medical School, Boston, United States; Precision Vaccines Program, Boston Children’s Hospital, Boston, United States
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.
