PXD040727 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | A rapid workflow for high-throughput FFPE-based quantitative proteomics |
| Description | Formalin-fixed, paraffin-embedded (FFPE) tissue samples are an invaluable resource to study the underlying molecular mechanisms of the diseases and when coupled with laser capture microdissection (LCM, isolation of sub histological regions of the tissue sections is readily obtained for further analysis. LCM-based FFPE tissue proteomics is gaining clinicopathological significance particularly in biomarker discovery driven research, beyond its conventional morphology-based application in laboratory diagnosis. Processing of laser capture microdissected tissue sections can be challenging for quantitative proteomic analysis due to lower amount of protein retrieved and losses during the sample processing. A robust, streamlined and automated sample preparation workflow for efficient processing of large cohort of LCM samples which is a primary requisite for biomarker type of studies is needed. Here, we propose a new sample processing workflow for processing of FFPE samples and enable scalable, automated extraction of clean peptides from unprocessed or H&E-stained FFPE tissue sections for deep bottom-up protein profiling and quantification. |
| HostingRepository | PRIDE |
| AnnounceDate | 2023-10-24 |
| AnnouncementXML | Submission_2023-10-24_13:00:29.070.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD040727 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | BenjaminMadden |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2023-03-09 08:42:49 | ID requested | |
| ⏵ 1 | 2023-10-24 13:00:29 | announced | |
| 2 | 2023-11-14 09:10:42 | announced | 2023-11-14: Updated project metadata. |
| 3 | 2024-10-22 06:10:17 | announced | 2024-10-22: Updated project metadata. |
Publication List
| 10.6019/PXD040727; |
| Pujari GP, Mangalaparthi KK, Madden BJ, Bhat FA, Charlesworth MC, French AJ, Sachdeva G, Daviso E, Thomann U, McCarthy P, Vasantgadkar S, Bhattacharyya D, Pandey A, A High-Throughput Workflow for FFPE Tissue Proteomics. J Am Soc Mass Spectrom, 34(7):1225-1229(2023) [pubmed] |
Keyword List
| submitter keyword: FFPE, tandem mass spectrometry, kidney, LCM |
Contact List
| AkhileshPandey |
|---|
| contact affiliation | Professor , department of Laboratory Medicine and pathology, Mayo Clinic |
| contact email | Pandey.Akhilesh@mayo.edu |
| lab head | |
| BenjaminMadden |
|---|
| contact affiliation | Mayo Clinic |
| contact email | madden.benjamin@mayo.edu |
| 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/2023/10/PXD040727 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD040727
- Label: PRIDE project
- Name: A rapid workflow for high-throughput FFPE-based quantitative proteomics
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