PXD003052

PXD003052 is an original dataset announced via ProteomeXchange.

Title	yeast membrane proteomics using Leu3 labelling
Description	The yeast signal peptide peptidase homologue Ypf1 functionally interacts with the ER-associated degradation (ERAD) factors Dfm1 and Doa10 to control the abundance of the zinc transporter Zrt1. Here we report that Ctr1 is another substrate for this degradation mechanism with deletion of Ypf1 leading to an accumulation of Ctr1. We describe in detail the usage of leucine metabolic labelling in yeast in order to monitor quantitative proteome alterations, e.g. upon removal of a protease. Since laboratory yeast strains are typically leucine auxotroph, metabolic labelling with trideuterated leucine (d3-leucine) is a straightforward, cost-effective, and ubiquitously applicable strategy for quantitative proteomic studies similar to the widely used arginine/lysine SILAC method for mammalian cells. We showcase the usage of advanced peptide quantification using the FeatureFinderMultiplex algorithm (part of the OpenMS software package) for robust and reliable quantification. Furthermore, we present an OpenMS bioinformatics data analysis workflow that combines accurate quantification with high proteome coverage. In order to enable visualization, peptide-mapping, and sharing of quantitative proteomic data, especially for membrane-spanning and cell-surface proteins, we further developed the web-application Proteator. Due to its simplicity and robustness, we expect metabolic leucine labelling in yeast to be of great interest to the research community.
HostingRepository	PRIDE
AnnounceDate	2016-04-12
AnnouncementXML	Submission_2016-07-25_00:12:07.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lars Nilse
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	3x(2)H labeled L-leucine; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-10-14 02:54:02	ID requested
1	2016-04-12 09:21:56	announced
⏵ 2	2016-07-25 00:12:09	announced	Updated publication reference for PubMed record(s): 27426920.

Nilse L, Avci D, Heisterkamp P, Serang O, Lemberg MK, Schilling O, Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1. Biochim Biophys Acta, 1864(10):1363-71(2016) [pubmed]

curator keyword: Biological

submitter keyword: yeast, membrane, proteomics, Leu3 labelling, ERAD

Oliver Schilling
contact affiliation	Institute of Molecular Medicine and Cell Research, University of Freiburg, D-79104 Freiburg, Germany
contact email	oliver.schilling@mol-med.uni-freiburg.de
lab head
Lars Nilse
contact affiliation	Freiburg University
contact email	l.nilse@dunelm.org.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/2016/04/PXD003052

PRIDE project URI

• PRIDE
  1. PXD003052
     1. Label: PRIDE project
     2. Name: yeast membrane proteomics using Leu3 labelling