PXD060417-1

PXD060417 is an original dataset announced via ProteomeXchange.

Title	A Standard Operating Procedure for Protein Extraction from Abdominal Aortic Aneurysm Tissue: Enhancing Proteomics Applications
Description	The identification of putative biomarkers for predicting abdominal aortic aneurysm (AAA) progression can be achieved through proteomic strategies, particularly with shotgun proteomics. However, the heterogeneity of AAA tissue poses challenges for tissue homogenization and protein extraction, compromising reproducibility, an essential factor for clinical translation. Thus, we aimed to optimize a protocol for AAA tissue homogenization and protein extraction and to develop a standard operating procedure (SOP) to maximize protein yield and foster reproducibility in the field. In this context, several experimental variables were systematically tested in a bead-beating method for tissue homogenisation, including bead size (1.4 mm versus 2.8 mm of diameter), the number of extraction cycles (one up to three), a bead-to-tissue mass ratio at 20, 30, or 40, the lysis buffer-to-tissue ratio (10, 15, or 20 μL/mg), and the lysis buffer composition (RIPA, Urea/thiourea, and HEPES). Optimal conditions for protein extraction were achieved using 1.4 mm zirconium dioxide beads in two homogenization cycles, with a bead-to-tissue mass ratio of 30:1 and a lysis buffer-to-tissue ratio of 20 μL lysis buffer per milligram of tissue, in 2 mL O-ring cryotubes. Depending on the purpose of downstream analysis, recommendations for the use of each lysis buffers were provided based on their specific performance across specific indexes. In this context, HEPES and Urea/Thiourea buffers are recommended for studies prioritizing quantification reproducibility, while RIPA buffer is advised for protein extraction reproducibility. As a proof of concept, the optimized SOP was applied to characterize the AAA tissue proteome and several processes and pathways relevant in AAA pathophysiology were highlighted, including blood coagulation, cellular responses to stress, neutrophil degranulation, wound healing, and pathways of the immune system. Additionally, the enrichment analysis identified ECM remodeling and platelet activation, and degranulation as strongly represented pathways across the functional analysis for each buffer, reinforcing their contribution to aneurysm pathophysiology. Hence, these findings demonstrated that the SOP is well-suited for identifying disease-relevant biomarkers and therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2026-01-05
AnnouncementXML	Submission_2026-01-04_16:18:46.796.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rui Vitorino
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-03 03:49:21	ID requested
⏵ 1	2026-01-04 16:18:47	announced

Baltazar T, Trindade F, Nogueira-Ferreira R, Vitorino R, Ferreira R, Domingues P, Leite-Moreira A, Dias-Neto M, Consortium VA, Yeung KK, Jongkind V, Rijken L, Zwetsloot S, Ayyalasomayajula V, Smorenburg S, Wolterink J, Marquering H, I, š, gum I, Ploem C, Catarinella F, Lee R, Bera KD, Raffort J, Lareyre F, Muller C, Koncar I, Tomic I, Matejevic D, Ž, ivkovi, ć M, Djuric T, Stankovic A, Venermo M, Tulamo R, Laivuori M, Behrendt CA, Smit N, Schijven M, van den Born BJ, Delewi R, A Standard Operating Procedure for Protein Extraction From Abdominal Aortic Aneurysm Tissue: Enhancing Proteomics Applications. Proteomics Clin Appl, 20(1):e70030(2026) [pubmed]

10.1002/prca.70030;

submitter keyword: abdominal aortic aneurysm

aortic tissue homogenization

protein extraction

proteomics

SOP

Fabio Trindade
contact affiliation	Faculty of Medicine of the University of Porto Alameda Prof. Hernâni Monteiro 4200-319 Porto, Portugal
contact email	ftrindade@med.up.pt
lab head
Rui Vitorino
contact affiliation	Universidade de Aveiro
contact email	rvitorino@ua.pt
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060417
     1. Label: PRIDE project
     2. Name: A Standard Operating Procedure for Protein Extraction from Abdominal Aortic Aneurysm Tissue: Enhancing Proteomics Applications