PXD011857

PXD011857 is an original dataset announced via ProteomeXchange.

Title	A Signal Amplification via Boosting with Isobaric Labeling Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells
Description	Despite recent advances in MS-based proteomics, comprehensive phosphoproteomics analysis of small populations of cells remains a daunting task, due primarily to the general lack of sufficient MS signals from such limited amounts of samples. In light of the unique multiplexing feature of isobaric labeling where the “total” peptide signal from all channels (or samples) triggers MS/MS for peptide identification while the reporter ions are providing quantitative information, we tested the concept of using a “boosting” sample (e.g., a biological sample mimicking the study samples) in such multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomics measurements in <100,000 of cells. Indeed, this simple yet effective signal amplification via boosting in isobaric labeling (SABIL) strategy increased the number of quantifiable phosphorylation sites by more than 4-fold and demonstrated good reproducibility in quantification with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment also demonstrated the ability of SABIL to differentiate different acute myeloid leukemia cells based on the phosphoproteome data acquired therein. Furthermore, in a pilot application this strategy enabled quantitative analysis of over 20,000 phosphorylation sites of human islet samples from individual donors following cytokine treatment. Together, this signal boosting strategy provides an attractive solution to comprehensive and quantitative phosphoproteomic characterization of relatively small populations of cells where traditional phosphoproteomics workflow falls short of sensitivity.
HostingRepository	jPOST
AnnounceDate	2019-03-15
AnnouncementXML	Submission_2022-09-18_03:51:52.819.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chia-Feng Tsia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine; L-methionine sulfoxide; unknown modification; unknown modification
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-27 09:58:40	ID requested
1	2019-03-15 08:24:26	announced
2	2021-02-04 17:13:42	announced	2021-02-04: Updated FTP location.
⏵ 3	2022-09-18 03:51:53	announced	2022-09-18: Updated FTP location.

Yi L, Tsai CF, Dirice E, Swensen AC, Chen J, Shi T, Gritsenko MA, Chu RK, Piehowski PD, Smith RD, Rodland KD, Atkinson MA, Mathews CE, Kulkarni RN, Liu T, Qian WJ, Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells. Anal Chem, 91(9):5794-5801(2019) [pubmed]

submitter keyword: IMAC, TMT, phosphoproteome,

Tao Liu and Wei-Jun Qian
lab head
Chia-Feng Tsia
contact affiliation	Kyoto University
dataset submitter

jPOST dataset URI

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.jpostdb.org/JPST000522/