PXD018411 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | FLEXIQuant-LF: Robust Regression to quantify protein modification extent in label-free proteomics data |
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 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. |
HostingRepository | PRIDE |
AnnounceDate | 2020-12-04 |
AnnouncementXML | Submission_2020-12-04_00:20:04.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Christoph Schlaffner |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-04-06 22:35:00 | ID requested | |
⏵ 1 | 2020-12-04 00:20:04 | announced | |
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 affiliation | Department of Pathology, Boston Children's Hospital, USA Department of Pathology, Harvard Medical School, USA |
contact email | hanno.steen@childrens.harvard.edu |
lab head | |
Christoph Schlaffner |
contact affiliation | Boston Children's Hospital; Harvard Medical School |
contact email | christoph.schlaffner@childrens.harvard.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD018411
- Label: PRIDE project
- Name: FLEXIQuant-LF: Robust Regression to quantify protein modification extent in label-free proteomics data