PXD059876

PXD059876 is an original dataset announced via ProteomeXchange.

Title	Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers
Description	Recent advances in “omics” technologies have opened the possibilities to discover novel biomarkers of meat quality, including the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef characterized by a high ultimate pH. The available studies characterized very few numbers of animals and using mostly gel-based proteomics. The present study uses for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteomes of DFD (pH24 ≥ 6.2) compared to CONTROL beef samples (5.4 ≤ pH24 ≤ 5.6) within the largest database of DFD/CONTROL beef samples to date (26 pairs of samples of the young Asturiana de los Valles bulls, n=52). The statistical comparison yielded 35 putative protein biomarkers that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA applied on the proteome data revealed 31 and 36 proteins with VIP > 2 respectively. The combination of these findings identified 16 common proteins linked with DFD beef, irrespective of the statistical method. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef.
HostingRepository	PRIDE
AnnounceDate	2025-07-31
AnnouncementXML	Submission_2025-07-31_02:13:59.774.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susana Bravo
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-16 04:41:33	ID requested
⏵ 1	2025-07-31 02:14:00	announced

10.1016/J.MEATSCI.2024.109618;

submitter keyword: Beef quality defects

Biological mechanisms

Dark-cutting

Protein biomarkers

Proteome

Shotgun proteomics.

Susana B
contact affiliation	Instituto de Investigaciones Sanitarias de Santiago de Compostela
contact email	Sbbravo@gmail.com
lab head
Susana Bravo
contact affiliation	FIDIS
contact email	sbbravo@gmail.com
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/2025/07/PXD059876

PRIDE project URI

• PRIDE
  1. PXD059876
     1. Label: PRIDE project
     2. Name: Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers