PXD008408

PXD008408 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic analysis of fresh-frozen human breast tissue and tumor samples using microLC-SWATH-MS
Description	Future improvements in the field of breast cancer prevention, diagnosis and treatment require deeper knowledge and better understanding of the molecular processes and signaling pathways that lead to the transformation of normal cells to cancer ones and the disease progression. Quantitative proteome profiling of fresh frozen breast tissue and tumor samples may accelerate and facilitate this process. Liquid chromatography (LC) hyphenated to tandem mass spectrometry (MS/MS) technique in data-independent SWATH acquisition mode is a powerful tool for such profiling, because all the precursor ions are fragmented there, which enables label-free identification and quantification of theoretically all proteins in the sample. In this study we performed microLC separation before SWATH-MS analysis. The spectral library, which is necessary for SWATH quantification of the investigated samples, consisted of proteins identified by protein database search of the MS/MS spectra obtained by the information-dependent acquisition (IDA) screening of both normal human breast tissue and breast tumor samples, which were additionally enriched in low abundant proteins by immunoaffinity depletion from 14 high abundant serum proteins. Using the described methodology we detected 547 proteins in all qualitative experiments, which served then as a spectral library for further label-free SWATH quantification of separate breast tumor and corresponding normal breast tissue samples of 8 patients. Among them, 299 proteins were successfully quantified. Levels of 188 of them varied significantly (p<0.05) between normal breast tissue and breast tumor samples. 31proteins were up-regulated and 14 were down-regulated at least two fold in breast tumors comparing to normal breast tissues.
HostingRepository	PRIDE
AnnounceDate	2026-03-16
AnnouncementXML	Submission_2026-03-16_04:45:00.488.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aleksandra Bogucka
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-11 03:15:03	ID requested
⏵ 1	2026-03-16 04:45:01	announced

10.3389/fmolb.2026.1739472;

Macur K, Bogucka AE, Fel-Tukalska A, Skokowski J, O, ł, dziej S, Czaplewska P, A label-free microLC-SWATH-MS methodology with immunoaffinity depletion of highly abundant serum proteins for quantitative proteomic comparison of fresh-frozen human normal breast tissue and tumor clinical specimens. Front Mol Biosci, 13():1739472(2026) [pubmed]

curator keyword: Biomedical

submitter keyword: breast tissue,fresh frozen, breast tumor, microLC, SWATH-MS, quantitative proteomics

Katarzyna Macur
contact affiliation	Laboratory of Mass Spectrometry, Core Facility Laboratories, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk
contact email	katarzyna.macur@biotech.ug.edu.pl
lab head
Aleksandra Bogucka
contact affiliation	Justus Liebig University Giessen
contact email	aleksandra.lewandowska@biotech.ug.edu.pl
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/2026/03/PXD008408

PRIDE project URI

• PRIDE
  1. PXD008408
     1. Label: PRIDE project
     2. Name: Quantitative proteomic analysis of fresh-frozen human breast tissue and tumor samples using microLC-SWATH-MS