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PXD018411 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleFLEXIQuant-LF: Robust Regression to quantify protein modification extent in label-free proteomics data
DescriptionImprovements 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 fully understand 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 prior knowledge of the type of modification. 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 approach of FLEXIQuant-LF to assess the modification extent in quantitative proteomics data provides a novel platform to better understand the function and regulation of PTMs in new experiments and reanalyzed data. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristoph Schlaffner
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-04-06 22:35:00ID requested
12020-12-04 00:20:04announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: PTM identification, PTM quantification, label-free quantification, peptide modification, mass spectrometry, DDa, DIA, modification stochiometry, software, open source
Contact List
Hanno Steen
contact affiliationDepartment of Pathology, Boston Children's Hospital, USA Department of Pathology, Harvard Medical School, USA
contact emailhanno.steen@childrens.harvard.edu
lab head
Christoph Schlaffner
contact affiliationBoston Children's Hospital; Harvard Medical School
contact emailchristoph.schlaffner@childrens.harvard.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
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