<<< Full experiment listing


PXD002694 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDirect and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring HUB_MAN C4PR_LIV
DescriptionDefining 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 enable 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 531 proteins with high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterPhilip Brownridge
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListOxidation; Carbamidomethyl
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-08-10 06:18:49ID requested
12015-12-11 01:31:56announced
22016-01-12 08:45:33announcedUpdated publication reference for PubMed record(s): 26750110.
32017-02-16 00:30:34announcedUpdated project metadata.
42017-10-24 00:48:45announcedUpdated project metadata.
Publication List
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]
Keyword List
curator keyword: Biological
submitter keyword: absolute quantification
selected reaction monitoring
stable-isotope labelling
tandem quadrupole
Contact List
Rob Beynon
contact affiliationHead of Biochemistry Centre for Proteome Research G44, Biosciences Building| Institute of Integrative Biology University of Liverpool Crown Street Liverpool L69 7ZB
contact emailrbeynon@liverpool.ac.uk
lab head
Philip Brownridge
contact affiliationUniversity of Liverpool
contact emailphilipjb@liv.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
[ + ]