PXD004410

PXD004410 is an original dataset announced via ProteomeXchange.

Title	Absolute Quantitification of Yeast proteins by SIL-SRM using the QconCAT technology
Description	Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference dataset quantifying over 1800 S. cerevisiae proteins by direct means using protein-specific stable-isotope labelled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The SRM-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ~100 million molecules-per-cell, a median of ~1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a 'gold-standard' reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.
HostingRepository	PeptideAtlas
AnnounceDate	2016-06-21
AnnouncementXML	Submission_2016-06-21_10:41:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Craig Lawless
SpeciesList	scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Xevo TQ-S

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-21 10:13:45	ID requested
⏵ 1	2016-06-21 10:41:40	announced

Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ, Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics, 15(4):1309-22(2016) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Craig Lawless
contact affiliation	University of Manchester
contact email	craig.lawless@manchester.ac.uk
dataset submitter
Simon Hubbard
contact affiliation	University of Manchester
contact email	simon.hubbard@manchester.ac.uk
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI