PXD042089

PXD042089 is an original dataset announced via ProteomeXchange.

Title	Deep quantification of substrate turnover defines protease subsite cooperativity. Working title: Massively parallel mapping of dipeptidyl peptidase cleavage sites reveals substrate motifs
Description	Proteases play a crucial role in processing or breaking down proteins. They exhibit varying levels of substrate specificity that determine their physiological or pharmacological functions. However, this specificity is not well-understood. To address this, we have developed hiMAPS (high-throughput mapping of protease cleavage sites), a mass spectrometry-based method that can survey tens of thousands of distinct peptides. By applying this approach to human DPP4 and C. elegans DPF-3, two prolyl peptidases from the Dipeptidyl Peptidase IV (DPPIV) family, we have derived quantitative models that confirm a strong preference for Pro and Ala in the penultimate (P1) position from the N-terminus, but also reveal differences in the relative preferences for other residues. The hiMAPS approach can be applied to other exoproteases using various cheap sources of highly diverse peptides. Additionally, we have observed that these proteases tolerate and accept substrates containing Thr and Ser at P1 position.
HostingRepository	PRIDE
AnnounceDate	2024-11-01
AnnouncementXML	Submission_2024-11-01_04:03:05.698.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jan Seebacher
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-09 09:24:11	ID requested
⏵ 1	2024-11-01 04:03:06	announced

Gudipati RK, Gaidatzis D, Seebacher J, Muehlhaeusser S, Kempf G, Cavadini S, Hess D, Soneson C, Gro, ß, hans H, Deep quantification of substrate turnover defines protease subsite cooperativity. Mol Syst Biol, 20(12):1303-1328(2024) [pubmed]

10.1038/s44320-024-00071-4;

submitter keyword: DPP4, TMT, dipeptidyl peptidase, HeLa digest, multiplexing, proteome discoverer, sequence motif,hiMAPS, einprot, DPF-3

Helge Grosshans
contact affiliation	Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
contact email	helge.grosshans@fmi.ch
lab head
Jan Seebacher
contact affiliation	FMI Basel
contact email	jan.seebacher@fmi.ch
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/2024/11/PXD042089

PRIDE project URI

• PRIDE
  1. PXD042089
     1. Label: PRIDE project
     2. Name: Deep quantification of substrate turnover defines protease subsite cooperativity. Working title: Massively parallel mapping of dipeptidyl peptidase cleavage sites reveals substrate motifs