PXD003770

PXD003770 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS profiling of sample processing optimization of formalin-fixed, paraffin embedded tissues
Description	Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled with MRM-MS (targeting 515 analytes) to evaluate quantitatively the performance of three extraction protocols in combination with three trypsin digestion protocols (9 processes). An optimum process based on RapiGest buffer extraction and urea-based digestion was identified. The optimized process is generally amenable and enables highly reproducible, multiplex, standardizable quantitative MRM in archival specimens.
HostingRepository	PRIDE
AnnounceDate	2016-07-25
AnnouncementXML	Submission_2016-07-25_07:23:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacob Kennedy
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-11 02:51:33	ID requested
⏵ 1	2016-07-25 07:23:42	announced

Dataset with its publication pending

curator keyword: Technical

submitter keyword: Human, breast cancer tumor tissue, FFPE, Velos

Paulovich, Amanda G
contact affiliation	Full Member, Clinical Research
contact email	apaulovi@fredhutch.org
lab head
Jacob Kennedy
contact affiliation	Fred Hutchinson Cancer Research Center
contact email	jkennedy@fhcrc.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/2016/07/PXD003770

PRIDE project URI

• PRIDE
  1. PXD003770
     1. Label: PRIDE project
     2. Name: LC-MS/MS profiling of sample processing optimization of formalin-fixed, paraffin embedded tissues