PXD060847

PXD060847 is an original dataset announced via ProteomeXchange.

Title	Comparative Analysis and Correlation of Cancer Hotspot Proteins and Cell Markers in Tumor-Normal Adjacent Breast and Kidney Samples Using RPPA and LC-MS – PRM data
Description	Despite the tremendous global effort in discovering and cataloguing somatic mutations in cancer-related genes and the impact they exert on human cancers, the effects of these mutations on the protein expression levels are inadequately addressed. Here, we evaluated the expression of proteins represented by the Ion AmpliSeq™ Cancer Hotspot Panel v2 and cell markers, in human breast and kidney tumor-normal adjacent samples. To this end, we employed two distinct proteomic techniques—Reverse Phase Protein Array (RPPA) and Liquid Chromatography-Mass Spectrometry (LC-MS). The latter was used in progressively advanced modes: data-dependent acquisition, data-independent acquisition, and parallel reaction monitoring, aiming to improve the quantitation of specific protein expression levels. Significant alterations in protein expression were observed using both methods, also revealing patient-specific proteomic profiles. Furthermore, both overlapping and unique findings between RPPA and LC-MS were observed, indicating their complementary nature. However, Spearman coefficient analysis demonstrated varying degrees of correlation between RPPA and LC-MS data. This integrated approach underscores the necessity of dual-platform analyses in cancer proteomics to improve diagnostic and therapeutic strategies. Our study aims to fill the gap in assessing the proteomic consequences of somatic mutations, suggesting a potential need for confirmation that a cancer related protein is up- or downregulated -and to what extent- by both RPPA and LC-MS to ensure robust and reliable findings.
HostingRepository	PRIDE
AnnounceDate	2026-09-07
AnnouncementXML	Submission_2026-09-06_16:32:50.184.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Potesil
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-15 14:45:15	ID requested
⏵ 1	2026-09-06 16:32:51	announced

Paal K, Karnok N, Konrad C, Bui D, Bugyi F, Turi, á, k L, Chinopoulos C, Comparative analysis and correlation of cancer hotspot proteins and cell markers in tumor-normal adjacent breast and kidney samples using RPPA and LC-MS. Sci Rep, 16(1):(2026) [pubmed]

10.1038/s41598-026-48754-2;

submitter keyword: proteomics,liquid chromatography–mass spectrometry, oncogene, tumor-suppressor gene

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
David Potesil
contact affiliation	Proteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech Republic
contact email	david.potesil@ceitec.muni.cz
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/PXD060847

PRIDE project URI

• PRIDE
  1. PXD060847
     1. Label: PRIDE project
     2. Name: Comparative Analysis and Correlation of Cancer Hotspot Proteins and Cell Markers in Tumor-Normal Adjacent Breast and Kidney Samples Using RPPA and LC-MS – PRM data