PXD001749

PXD001749 is an original dataset announced via ProteomeXchange.

Title	Targeted Proteome Pipeline and Assay for 112 Rat Brain Synaptic Proteins, Data Collection
Description	We present a comprehensive workflow for large scale (>1000 transitions/run) label-free LC-MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling (xMRM) that improves Signal/Noise by >2-fold, and automatic peak modeling. Improvements to data analysis, including a novel Q/C metric, Normalized Group Area Ratio (NGAR), MLR normalization, weighted regression analysis, and data dissemination through the Yale Protein Expression Database. As a proof of principal we developed a robust 90 minute LC-MRM assay for Mouse/Rat Post-Synaptic Density (PSD) fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (0.997) and protein fold change (0.94) between the label-free and SIS analyses. Overall, our first method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay.
HostingRepository	PeptideAtlas
AnnounceDate	2015-01-29
AnnouncementXML	Submission_2015-01-29_13:04:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Colangelo
SpeciesList	scientific name: Rattus norvegicus; NCBI TaxID: 10116;
ModificationList	S-carboxamidomethyl-L-cysteine
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-28 15:26:40	ID requested
⏵ 1	2015-01-29 13:04:17	announced

Colangelo CM, Ivosev G, Chung L, Abbott T, Shifman M, Sakaue F, Cox D, Kitchen RR, Burton L, Tate SA, Gulcicek E, Bonner R, Rinehart J, Nairn AC, Williams KR, Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins. Proteomics, 15(7):1202-14(2015) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Christopher Colangelo
contact affiliation	Yale University
contact email	christopher.colangelo@yale.edu
dataset submitter
Christopher Colangelo
contact affiliation	Yale University
contact email	christopher.colangelo@yale.edu
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI

PASSEL transition group browser URI