PXD001823

PXD001823 is an original dataset announced via ProteomeXchange.

Title	Feasibility of protein turnover studies in prototroph yeast
Description	Quantitative proteomics studies of yeast that use metabolic labeling with amino acids rely on auxotrophic mutations of one or more genes on the amino acid biosynthesis pathways. These mutations affect yeast metabolism, and preclude the study of some biological processes. Overcoming this limitation, it has recently been described that proteins in a yeast prototrophic strain can also be metabolically labeled with heavy amino acids. However, the temporal profiles of label incorporation under the different phases of the prototroph’s growth have not been examined. Labeling trajectories are important in the study of protein turnover and dynamics, in which label incorporation into proteins is monitored across many timepoints. Here we monitored protein labeling trajectories for 48 h after a pulse with heavy lysine in a yeast prototrophic strain and compared them with those of a lysine auxotrophic yeast. Labeling was successful in prototroph yeast during exponential growth phase but not in stationary phase. Furthermore, we were able to determine the half lives of more than 1,700 proteins during exponential phase of growth with high accuracy and reproducibility. We found a median half life of 2 h in both strains which corresponds with the cellular doubling time. Nucleolar and ribosomal proteins showed short half-lives whereas mitochondrial proteins and other energy production enzymes presented longer half-lives. Except for some proteins involved in lysine biosynthesis, we observed a high correlation in protein half lives between prototroph and auxotroph strains. Overall, our results demonstrate the feasibility of using prototrophs for proteomic turnover studies and provide a reliable dataset of protein half lives in exponentially growing yeast.
HostingRepository	PRIDE
AnnounceDate	2015-03-27
AnnouncementXML	Submission_2015-03-27_07:15:11.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Martin Perez
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-02-18 00:57:58	ID requested
⏵ 1	2015-03-27 07:15:12	announced

Martin-Perez M, Vill, é, n J, Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains. Anal Chem, 87(7):4008-14(2015) [pubmed]

curator keyword: Biological

submitter keyword: Saccharomyces cerevisiae, yeast, Qexactive, LC-MS/MS, native SILAC, pulsed SILAC, protein half life

Judit Villen
contact affiliation	Department of Genome Sciences University of Washington 3720 15th Ave NE Seattle WA 98195 (USA)
contact email	jvillen@u.washington.edu
lab head
Miguel Martin Perez
contact affiliation	University of Washington
contact email	mmarper@uw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001823
     1. Label: PRIDE project
     2. Name: Feasibility of protein turnover studies in prototroph yeast