PXD038277

PXD038277 is an original dataset announced via ProteomeXchange.

Title	In-depth specificity profiling of Pro-Pro endopeptidases (PPEPs) using combinatorial synthetic peptide libraries
Description	Proteases comprise the class of enzymes that catalyze the hydrolysis of peptide bonds, thereby playing a pivotal role in many aspects of life. The amino acids surrounding the scissile bond determine the susceptibility towards protease-mediated hydrolysis. A detailed understanding of the cleavage specificity of a protease can lead to the identification of its endogenous substrates, while it is also essential for the design of inhibitors. We developed a new method which combines the high diversity of a combinatorial synthetic peptide library with the sensitivity and detection power of mass spectrometry to determine protease cleavage specificity. We applied this method to study a group of bacterial metalloproteases that have the unique specificity to cleave between two prolines, i.e. Pro-Pro endopeptidases (PPEPs). We not only confirmed the prime-side specificity of PPEP-1 and PPEP-2, but also revealed some new unexpected peptide substrates. Moreover, we have characterized a new PPEP (PPEP-3) which has a prime-side specificity that is very different from that of the other two PPEPs. Importantly, the approach that we present in this study is generic and can be extended to investigate the specificity of other proteases.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:04:25.689.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yassene Mohammed
SpeciesList	scientific name: Geobacillus stearothermophilus; NCBI TaxID: 1422; scientific name: Clostridioides difficile; NCBI TaxID: 1496; scientific name: Paenibacillus alvei DSM 29; NCBI TaxID: 1206781;
ModificationList	biotinylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-22 03:27:21	ID requested
1	2023-08-01 01:35:41	announced
⏵ 2	2023-11-14 09:04:34	announced	2023-11-14: Updated project metadata.

Claushuis B, Cordfunke RA, de Ru AH, Otte A, van Leeuwen HC, Klychnikov OI, van Veelen PA, Corver J, Drijfhout JW, Hensbergen PJ, In-Depth Specificity Profiling of Endopeptidases Using Dedicated Mix-and-Split Synthetic Peptide Libraries and Mass Spectrometry. Anal Chem, 95(31):11621-11631(2023) [pubmed]

submitter keyword: Pro-Pro endopeptidase, specificity profiling, mass spectrometry (MS), PPEP, synthetic peptide libraries, substrate specificity, high-performance liquid chromatography (HPLC), FRET peptides, metalloprotease

Paul J. Hensbergen
contact affiliation	Center for Proteomics and Metabolomics, LUMC, Leiden, The Netherlands
contact email	p.j.hensbergen@lumc.nl
lab head
Yassene Mohammed
contact affiliation	LUMC/UVIC
contact email	y.mohammed@lumc.nl
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/2023/08/PXD038277

PRIDE project URI

• PRIDE
  1. PXD038277
     1. Label: PRIDE project
     2. Name: In-depth specificity profiling of Pro-Pro endopeptidases (PPEPs) using combinatorial synthetic peptide libraries