PXD046169

PXD046169 is an original dataset announced via ProteomeXchange.

Title	Kinase Inhibitor Pulldown Assay (KiP) for Clinical Proteomics (SureQuant)
Description	Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential, but current approaches are inadequate. For breast cancer treatment for example, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers more quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of protein yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_06:37:13.591.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Holt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-16 15:55:58	ID requested
⏵ 1	2024-01-26 06:37:14	announced

10.1186/s12014-023-09448-3;

Saltzman AB, Chan DW, Holt MV, Wang J, Jaehnig EJ, Anurag M, Singh P, Malovannaya A, Kim BJ, Ellis MJ, Kinase inhibitor pulldown assay (KiP) for clinical proteomics. Clin Proteomics, 21(1):3(2024) [pubmed]

submitter keyword: Breast Cancer, IS-PRM,SureQuant, KiP

Matthew Holt
contact affiliation	Baylor College of Medicine
contact email	mvholt@bcm.edu
lab head
Matthew Holt
contact affiliation	BCM
contact email	mvholt@bcm.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/2024/01/PXD046169

PRIDE project URI

• PRIDE
  1. PXD046169
     1. Label: PRIDE project
     2. Name: Kinase Inhibitor Pulldown Assay (KiP) for Clinical Proteomics (SureQuant)