PXD019764

PXD019764 is an original dataset announced via ProteomeXchange.

Title	Lowering Sample Requirements to Study Tyrosine Kinase Signaling using Phosphoproteomics with the TMT Calibrator Approach
Description	Analysis of tyrosine kinase signaling is critical for the development of targeted cancer therapy. Currently, immunoprecipitation (IP) of phosphotyrosine (pY) peptides prior to liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to profile kinase substrates. A typical protocol requests 10 mg of total protein from ~108 cells or 50-100 mg of tissue. Large sample requirements can be cost prohibitive or not feasible for certain experiments. Sample multiplexing in chemical labeling reduces the protein amount required for each sample, and newer approaches use a material-rich reference channel as a calibrator to trigger detection and quantification for smaller samples. Here, we demonstrate that the tandem mass tag (TMT) calibrator approach reduces the sample input for pY profiling 10-fold (to ~1 mg total protein per sample from 107 cells grown in one plate), while maintaining the depth of pY proteome sampling and the biological content of the experiment. This strategy opens more opportunities for pY profiling of large sample cohorts and samples with limited protein quantity such as immune cells, xenograft models, and human tumors.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:10:08.257.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019764
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	John Koomen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-15 02:49:02	ID requested
1	2020-07-28 22:55:14	announced
2	2020-09-08 23:16:45	announced	2020-09-09: Updated publication reference for PubMed record(s): 32865326.
⏵ 3	2024-10-22 05:10:16	announced	2024-10-22: Updated project metadata.

10.1002/pmic.202000116;

10.6019/PXD019764;

Fang B, Izumi V, Rix LLR, Welsh E, Pike I, Reuther GW, Haura EB, Rix U, Koomen JM, Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach. Proteomics, 20(24):e2000116(2020) [pubmed]

submitter keyword: Signaling, Phosphotyrosine,Label Free Quantification, Lung Cancer, LC-MS/MS

John M. Koomen, PhD
contact affiliation	Moffitt Cancer Center Tampa, FL, USA
contact email	john.koomen@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/2020/07/PXD019764

PRIDE project URI

• PRIDE
  1. PXD019764
     1. Label: PRIDE project
     2. Name: Lowering Sample Requirements to Study Tyrosine Kinase Signaling using Phosphoproteomics with the TMT Calibrator Approach