PXD027970

PXD027970 is an original dataset announced via ProteomeXchange.

Title	multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-free Proteomics Datasets
Description	In high-throughput LC-MS/MS-based proteomics, information about the presence and stoichiometry of post-translational modifications is normally not readily available. To overcome this problem we developed multiFLEX-LF, a computational tool that builds upon FLEXIQuant and FLEXIQuant-LF, which detect modified peptides and quantify their modification extent by monitoring the differences between observed and expected intensities of the unmodified peptides. To this end, multiFLEX-LF relies on robust linear regression to calculate the modification extent of a given peptide relative to a within-study reference. multiFLEX-LF can analyze entire label-free discovery proteomics datasets. Furthermore, to analyze modification dynamics and co-regulated modifications, the peptides of all proteins are hierarchically clustered based on their computed relative modification scores. To demonstrate the versatility of multiFLEX-LF we applied it on a cell-cycle time series dataset acquired using data-independent acquisition. The clustering of the peptides highlighted several groups of peptides with different modification dynamics across the four analyzed time points providing evidence of the kinases involved in the cell-cycle. Overall, multiFLEX-LF enables fast identification of potentially differentially modified peptides and quantification of their differential modification extent in large datasets. Additionally, multiFLEX-LF can drive large-scale investigation of modification dynamics of peptides in time series and case-control studies. multiFLEX-LF is available at https://gitlab.com/SteenOmicsLab/multiflex-lf.
HostingRepository	PRIDE
AnnounceDate	2022-02-11
AnnouncementXML	Submission_2022-02-11_06:36:10.522.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; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-17 04:05:44	ID requested
1	2022-02-11 06:33:02	announced
⏵ 2	2022-02-11 06:36:11	announced	2022-02-11: Updated publication reference for PubMed record(s): 35086334.

Hiort P, Schlaffner CN, Steen JA, Renard BY, Steen H, multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-Free Proteomics Data Sets. J Proteome Res, 21(4):899-909(2022) [pubmed]

submitter keyword: LC-MSMS, DIA, cell cycle, PTM stochiometry, post-translational modifications, quantification

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/2022/02/PXD027970

PRIDE project URI

• PRIDE
  1. PXD027970
     1. Label: PRIDE project
     2. Name: multiFLEX-LF: A Computational Approach to Quantify the Modification Stoichiometries in Label-free Proteomics Datasets