PXD074156-1

PXD074156 is an original dataset announced via ProteomeXchange.

Title	High-Throughput Acoustic FFPE Proteomics Reveals ATP5IF1-Associated Mitochondrial Remodeling in Acral Melanoma
Description	Formalin-fixed, paraffin-embedded (FFPE) archives underpin dermatopathology and translational oncology, enabling clinically annotated melanoma cohorts, but cohort-scale proteomics remains limited by labor and variability in upstream processing. We established a plate-scale, acoustic FFPE proteomics workflow and integrated it with AI-assisted digital pathology to support composition-aware molecular profiling from routine sections. The optimized pipeline reduces handling steps, improves reproducibility, and supports rapid parallel processing in a 96-well format. Deep data-independent acquisition mass spectrometry of 40 primary melanomas spanning acral lentiginous, lentigo maligna, superficial spreading, and nodular subtypes quantified more than 8,200 protein groups and a mean of 5,200 proteins per tumor. Proteome profiles resolved melanoma subtypes and defined an acral lentiginous melanoma program enriched for translation/biogenesis and extracellular matrix/adhesion processes with relative depletion of lipid and fatty-acid metabolism and peroxisomal pathways. Supervised feature selection highlighted TNC, POSTN, EIF4A1, and ARF4 and uncovered selective depletion of ATP5IF1, a regulator of mitochondrial ATP synthase, in acral lentiginous melanoma. ATP5IF1 depletion persisted after adjustment for mitochondrial proxies and coincided with higher glycolysis relative to Complex V. This pathology-integrated, high-throughput FFPE proteomics framework enables scalable retrospective discovery and reveals subtype-specific mitochondrial remodeling in an underrepresented melanoma subtype.
HostingRepository	PRIDE
AnnounceDate	2026-09-09
AnnouncementXML	Submission_2026-09-09_01:47:27.962.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeovanis Gil
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2026-02-06 11:20:42	ID requested
⏵ 1	2026-09-09 01:47:29	announced

Fern, á, ndez-Coto DL, Ayala M, Alonso R, Palmqvist A, Garc, í, a MF, Balderas-L, ó, pez SF, Oskolas H, Christersson L, Ful, ö, p L, Szigeti B, Olivera-Rodr, í, guez VH, Marko-Varga M, Horvatovich P, Malm J, Szadai L, Herrera-Goepfert R, Szasz AM, Encarnaci, ó, n-Guevara S, Marko-Varga G, Gil J, High-Throughput Acoustic FFPE Proteomics Reveals ATP5IF1-Associated Mitochondrial Alterations in Acral Melanoma. Mol Cell Proteomics, 25(8):101620(2026) [pubmed]

10.1016/j.mcpro.2026.101620;

submitter keyword: AI-Digital Pathology

ATP synthase inhibitor IF1

Adaptive focused acoustics

Acral melanoma, Oxidative phosphorylation

Plate-scale FFPE proteomics

Jeovanis Gil
contact affiliation	Department of Translational Medicine, Lund University, Lund Sweden
contact email	jeovanis.gil_valdes@med.lu.se
lab head
Jeovanis Gil
contact affiliation	Lund University
contact email	jeovanis.gil_valdes@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/2026/09/PXD074156

PRIDE project URI

• PRIDE
  1. PXD074156
     1. Label: PRIDE project
     2. Name: High-Throughput Acoustic FFPE Proteomics Reveals ATP5IF1-Associated Mitochondrial Remodeling in Acral Melanoma