PXD018411-2

PXD018411 is an original dataset announced via ProteomeXchange.

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	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:16:10.668.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

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-06 22:35:00	ID requested
1	2020-12-04 00:20:04	announced
⏵ 2	2024-10-22 05:16:11	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: DIA, mass spectrometry, modification stochiometry, peptide modification, software, PTM quantification,PTM identification, open source, label-free quantification, DDa

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD018411

PRIDE project URI

• PRIDE
  1. PXD018411
     1. Label: PRIDE project
     2. Name: FLEXIQuant-LF: Robust Regression to quantify protein modification extent in label-free proteomics data