PXD004413

PXD004413 is an original dataset announced via ProteomeXchange.

Title	Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS) C4PR_LIV
Description	Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure, with high confidence, turnover rates are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared to selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data is acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focussed studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.
HostingRepository	PRIDE
AnnounceDate	2017-02-16
AnnouncementXML	Submission_2017-02-16_00:30:49.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004413
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephen Holman
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	Oxidation; Label:13C(6); Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-22 01:31:29	ID requested
1	2016-08-10 06:56:46	announced
⏵ 2	2017-02-16 00:30:49	announced	Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Protein turnover, SRM, MS1, proteomics, quantification, mass spectrometry

Robert J. Beynon
contact affiliation	Centre for Proteome Research, Department of Biochemistry, University of Liverpool, UK
contact email	r.beynon@liv.ac.uk
lab head
Stephen Holman
contact affiliation	University of Liverpool
contact email	stephen.holman@liverpool.ac.uk
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/2016/08/PXD004413

PRIDE project URI

• PRIDE
  1. PXD004413
     1. Label: PRIDE project
     2. Name: Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS) C4PR_LIV