PXD036910
PXD036910 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2022-09-21 15:10:22 | ID requested | |
⏵ 1 | 2024-05-21 13:07:33 | announced |
Publication List
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] |
Keyword List
submitter keyword: pediatric tumors,Trifluoroacetic acid, FFPE, sonication-free, clinical proteomics |
Contact List
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 |
Full Dataset Link List
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 |
Repository Record List
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