PXD048892-1

PXD048892 is an original dataset announced via ProteomeXchange.

Title	Community-based peptidomic clustering reveals pathogen-specific proteolytic signatures in wounds
Description	Recent advances in mass spectrometry-based peptidomics has catalyzed the identification and quantification of thousands endogenous peptides across diverse biological systems. However, the large theoretical peptidomic landscape and high proportion of missing values poses several challenges for downstream analyses and limits the comparability of clinical samples. Here, we present a generalizable computational workflow that clusters peptides with overlapping sequences to reduce the dimensionality of peptidomic data, improve the definition of protease cut-sites, enhance inter-sample comparability, and enable the implementation of reliable and 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 wounds and human clinical non-healing wounds. The analysis revealed signature phenotype-specific peptide regions reflecting pathogen-specific proteolytic activity at the earliest stages of colonization, resulting in novel class of potential peptide cluster-based biomarkers.
HostingRepository	PRIDE
AnnounceDate	2024-07-13
AnnouncementXML	Submission_2024-07-13_04:09:29.861.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

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PRIDE project URI

• PRIDE
  1. PXD048892
     1. Label: PRIDE project
     2. Name: Community-based peptidomic clustering reveals pathogen-specific proteolytic signatures in wounds