PXD066029

PXD066029 is an original dataset announced via ProteomeXchange.

Title	Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage
Description	In this study, we present a robust and scalable sample preparation protocol based on chemical lysis with trifluoroacetic acid (TFA), adapted from the SPEED method and optimized for human skin samples. The protocol simplifies tissue lysis while selectively leaving ECM scaffolds largely insoluble. As a result, abundant collagens and structural proteins are effectively depleted from the soluble fraction, improving the dynamic range of detectable proteins and increasing sensitivity for less abundant species. Using TFA lysis followed by solid-phase-enhanced sample preparation (SP3), we identified up to 6,200 protein groups from full-thickness human skin punch biopsies. Notably, the protocol enables high-depth proteomic analysis from 2 mm punch biopsies, which are less invasive and more suitable for longitudinal or large-cohort studies. Tape strip samples—commonly used in dermatological research for minimally invasive epidermal sampling—were also compatible with this protocol, yielding up to 2,300 protein groups, representing a two- to threefold increase compared to previously reported studies.
HostingRepository	PRIDE
AnnounceDate	2025-08-21
AnnouncementXML	Submission_2025-08-21_06:56:06.217.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Max Sauerland
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-10 13:04:44	ID requested
⏵ 1	2025-08-21 06:56:06	announced

Dataset with its publication pending

submitter keyword: tape strip,proteomics, skin, SPEED, scalable, ubiquitin

Mads Gyrd-Hansen
contact affiliation	LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, DK
contact email	mgyrd@sund.ku.dk
lab head
Max Sauerland
contact affiliation	University of Copenhagen
contact email	max.sauerland@sund.ku.dk
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/2025/08/PXD066029

PRIDE project URI

• PRIDE
  1. PXD066029
     1. Label: PRIDE project
     2. Name: Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage