PXD008512

PXD008512 is an original dataset announced via ProteomeXchange.

Title	Systematic analysis of protein turnover in primary cells - Part IV
Description	To better understand proteostasis in health and disease, determination of protein half-lives is essential. We improved the precision and accuracy of peptide-ion intensity based quantification in order to enable accurate determination of protein turnover in non-dividing cells using dynamic-SILAC. This enabled precise and accurate protein half-life determination ranging from 10 to more than 1000 hours. We achieve good proteomic coverage ranging from four to six thousand proteins in several types of non-dividing cells, corresponding to a total of 9699 unique proteins over the entire dataset. Good agreement was observed in half-lives between B-cells, natural killer cells and monocytes, while hepatocytes and mouse embryonic neurons showed substantial differences. Our comprehensive dataset enabled extension and statistical validation of the previous observation that subunits of protein complexes tend to have coherent turnover. Furthermore, we observed complex architecture dependent turnover within complexes of the proteasome and the nuclear pore complex. Our method is broadly applicable and might be used to investigate protein turnover in various cell types.
HostingRepository	PRIDE
AnnounceDate	2018-06-08
AnnouncementXML	Submission_2018-06-08_08:41:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maria Faelth Savitski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methionine oxidation with neutral loss of 64 Da; 6x(13)C: 2x(15)N labeled L-lysine; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-20 01:58:13	ID requested
⏵ 1	2018-06-08 08:41:57	announced

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM, Systematic analysis of protein turnover in primary cells. Nat Commun, 9(1):689(2018) [pubmed]

curator keyword: Biological

submitter keyword: protein half lives, SILAC, hepatocytes, isobarQuant

Marcus Bantscheff
contact affiliation	Cellzome
contact email	marcus.x.bantscheff@gsk.com
lab head
Maria Faelth Savitski
contact affiliation	Cellzome
contact email	maria.x.faelth-savitski@gsk.com
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/2018/06/PXD008512

PRIDE project URI

• PRIDE
  1. PXD008512
     1. Label: PRIDE project
     2. Name: Systematic analysis of protein turnover in primary cells - Part IV