PXD036910-1

PXD036910 is an original dataset announced via ProteomeXchange.

Title	ASAP – Automated Sonication free Acid assisted Proteomes from cells & FFPE tissues
Description	Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies but protein extraction and subsequent sample processing steps have shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows and analysis pipelines yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for Automated Sonication-free Acid-assisted Proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens achieving similar proteome coverage as established methods using time in equipment-heavy sonication-based methods at reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.
HostingRepository	PRIDE
AnnounceDate	2024-05-21
AnnouncementXML	Submission_2024-05-21_13:07:32.376.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Philipp Lange
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-21 15:10:22	ID requested
⏵ 1	2024-05-21 13:07:33	announced

10.1021/acs.analchem.2c04264;

Barnabas GD, Goebeler V, Tsui J, Bush JW, Lange PF, from Cells and FFPE Tissues. Anal Chem, 95(6):3291-3299(2023) [pubmed]

submitter keyword: pediatric tumors,Trifluoroacetic acid, FFPE, sonication-free, clinical proteomics

Philipp Lange
contact affiliation	Department of Pathology, University of British Columbia, Vancouver, BC, Canada
contact email	philipp.lange@ubc.ca
lab head
Philipp Lange
contact affiliation	University of British Columbia
contact email	philipp.lange@ubc.ca
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/2024/05/PXD036910

PRIDE project URI

• PRIDE
  1. PXD036910
     1. Label: PRIDE project
     2. Name: ASAP – Automated Sonication free Acid assisted Proteomes from cells & FFPE tissues