PXD045879

PXD045879 is an original dataset announced via ProteomeXchange.

Title	Accelerating Sample Preparation for Proteomics of Formalin Fixed Paraffin Embedded Tumor Tissues to Enable Biomarker Analysis
Description	Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the crosslinking and pre-analytical variables, these samples have been demonstrated to be useful for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients’ medical histories. Proteomics of formalin fixed paraffin embedded (FFPE) tissues also integrates with histological and molecular pathology strategies, so that additional biopsies or resected tumor aliquots do not need to be used. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the sample preparation for FFPE can be onerous, particularly for very precious (i.e., limited) samples. Therefore, we compared a modified version of the well-established filter-aided sample preparation strategy to a recently introduced kit-based EasyPep method using laser capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables, while also enabling the development of methods for spatial proteomics to examine intratumoral heterogeneity.
HostingRepository	PRIDE
AnnounceDate	2023-11-28
AnnouncementXML	Submission_2023-11-28_12:21:45.625.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	John Koomen
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-03 08:47:47	ID requested
⏵ 1	2023-11-28 12:21:46	announced

Dataset with its publication pending

submitter keyword: TMT,FFPE, Lung Adenocarcinoma, FASP, Expression Proteomics, EasyPep

Elsa Flores
contact affiliation	Molecular Oncology Moffitt Cancer Center Tampa, FL, USA
contact email	elsa.flores@moffitt.org
lab head
John Koomen
contact affiliation	Moffitt Cancer Center
contact email	john.koomen@moffitt.org
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/2023/11/PXD045879

PRIDE project URI

• PRIDE
  1. PXD045879
     1. Label: PRIDE project
     2. Name: Accelerating Sample Preparation for Proteomics of Formalin Fixed Paraffin Embedded Tumor Tissues to Enable Biomarker Analysis