PXD048892

PXD048892 is an original dataset announced via ProteomeXchange.

Title	Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data
Description	Recent advances in mass spectrometry-based peptidomics have catalyzed the identification and quantification of thousands of endogenous peptides across diverse biological systems. However, the vast peptidomic landscape generated by proteolytic processing poses several challenges for downstream analyses and limits the comparability of clinical samples. Here, we present an algorithm that aggregates peptides into peptide clusters, reducing the dimensionality of peptidomics data, improving the definition of protease cut sites, enhancing inter-sample comparability, and enabling the implementation of large-scale data analysis methods akin to those employed in other omics fields. We showcase the algorithm by performing large-scale quantitative analysis of wound fluid peptidomes of highly defined porcine wound infections and human clinical non-healing wounds. This revealed signature phenotype-specific peptide regions and proteolytic activity at the earliest stages of bacterial colonization. We validated the method on the urinary peptidome of type 1 diabetics which revealed potential subgroups and improved classification accuracy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:49:37.863.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD048892
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Fredrik Forsberg
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-25 09:13:06	ID requested
1	2024-07-13 04:09:30	announced
2	2024-07-16 06:21:19	announced	2024-07-16: Updated project metadata.
⏵ 3	2024-10-22 06:49:38	announced	2024-10-22: Updated project metadata.

10.6019/PXD048892;

submitter keyword: peptidomics, wound fluid,Peptides, human, infection, porcine

Artur Schmidtchen
contact affiliation	Dermatology and Venereology, Lund University, Sweden
contact email	artur.schmidtchen@med.lu.se
lab head
Fredrik Forsberg
contact affiliation	Lund University
contact email	fredrik.forsberg@med.lu.se
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/2024/07/PXD048892

PRIDE project URI

• PRIDE
  1. PXD048892
     1. Label: PRIDE project
     2. Name: Peptide clustering enhances large-scale analyses and reveals proteolytic signatures in mass spectrometry data