PXD002694

PXD002694 is an original dataset announced via ProteomeXchange.

Title	Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring HUB_MAN C4PR_LIV
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 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.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_00:48:43.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002694
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Philip Brownridge
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-10 06:18:49	ID requested
1	2015-12-11 01:31:56	announced
2	2016-01-12 08:45:33	announced	Updated publication reference for PubMed record(s): 26750110.
3	2017-02-16 00:30:34	announced	Updated project metadata.
⏵ 4	2017-10-24 00:48:45	announced	Updated project metadata.

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: Biological

submitter keyword: absolute quantification

selected reaction monitoring

SRM

stable-isotope labelling

yeast

tandem quadrupole

QconCAT

Rob Beynon
contact affiliation	Head of Biochemistry Centre for Proteome Research G44, Biosciences Building| Institute of Integrative Biology University of Liverpool Crown Street Liverpool L69 7ZB
contact email	rbeynon@liverpool.ac.uk
lab head
Philip Brownridge
contact affiliation	University of Liverpool
contact email	philipjb@liv.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002694
     1. Label: PRIDE project
     2. Name: Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring HUB_MAN C4PR_LIV