PXD040727

PXD040727 is an original dataset announced via ProteomeXchange.

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	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:10:15.552.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD040727
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Benjamin Madden
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

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.

10.1021/jasms.3c00099;

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]

submitter keyword: FFPE, tandem mass spectrometry, kidney, LCM

Akhilesh Pandey
contact affiliation	Professor , department of Laboratory Medicine and pathology, Mayo Clinic
contact email	Pandey.Akhilesh@mayo.edu
lab head
Benjamin Madden
contact affiliation	Mayo Clinic
contact email	madden.benjamin@mayo.edu
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/2023/10/PXD040727

PRIDE project URI

• PRIDE
  1. PXD040727
     1. Label: PRIDE project
     2. Name: A rapid workflow for high-throughput FFPE-based quantitative proteomics