PXD013966

PXD013966 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS of MDA-MB468 breast cancer cells grown under normal and glucose deprivation conditions
Description	Mass spectrometry-based spectral count has been a common choice of label-free proteome quantification as its simplicity for the sample preparation and data generation. The discriminatory nature of spectral count in the MS data-dependent acquisition, however, inherently introduces the spectral count variation for low-abundance proteins in multiplicative LC-MS/MS analysis, which hampers sensitive proteome quantification. We implemented the error model in the spectral count refinement as a post PLGEM-STN for improving sensitivity for quantitation of low-abundance proteins by reducing spectral count variability. In the statistical framework, automated spectral count refinement by integrating the two statistical tools was tested with triplicate LC-MS/MS datasets of MDA-MB468 breast cancer cells grown under normal and glucose deprivation conditions. We identified about 30% more quantifiable proteins that were found to be low-abundance proteins, which were initially filtered out by the PLGEM-STN analysis.
HostingRepository	PRIDE
AnnounceDate	2019-09-25
AnnouncementXML	Submission_2019-09-25_05:45:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hayun Lee
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-22 03:13:06	ID requested
⏵ 1	2019-09-25 05:45:09	announced

Lee HY, Kim EG, Jung HR, Jung JW, Kim HB, Cho JW, Kim KM, Yi EC, Refinements of LC-MS/MS Spectral Counting Statistics Improve Quantification of Low Abundance Proteins. Sci Rep, 9(1):13653(2019) [pubmed]

submitter keyword: LC.MS/MS, label-free, breast cancer

Eugene C. Yi
contact affiliation	Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, 03080, South Korea
contact email	euyi@snu.ac.kr
lab head
Hayun Lee
contact affiliation	Seoul National University
contact email	hayun.lee@snu.ac.kr
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/2019/09/PXD013966

PRIDE project URI

• PRIDE
  1. PXD013966
     1. Label: PRIDE project
     2. Name: LC-MS/MS of MDA-MB468 breast cancer cells grown under normal and glucose deprivation conditions