PXD010859

PXD010859 is an original dataset announced via ProteomeXchange.

Title	Precisely measured protein lifetimes in the mouse
Description	The turnover of brain proteins is critical for organism survival, and its perturbations are strongly linked to pathology. Nevertheless, precise protein lifetimes have been difficult to obtain in vivo. They are readily measured in vitro by feeding cells with isotopically-labeled amino acids, followed by mass spectrometry analyses. In vivo proteins are generated from at least two sources: labeled amino acids from the diet, and non-labeled amino acids from the degradation of pre-existing proteins. This renders measurements difficult. We solved this problem rigorously by developing a novel workflow that combines mouse in vivo isotopic labeling with mass spectrometry and mathematical modeling. We also established several independent approaches to test and validate the results. This enabled us to measure, for the first time, the accurate lifetimes of ~3500 brain proteins. The high precision of our data provided a large set of biologically-significant observations, including pathway-, organelle-, organ-, or cell-specific effects, along with a comprehensive catalogue of stable proteins, including novel extremely long-lived proteins (ELLPs).
HostingRepository	PRIDE
AnnounceDate	2018-12-04
AnnouncementXML	Submission_2018-12-04_04:07:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sunit Mandad
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-24 02:00:45	ID requested
1	2018-11-21 02:44:38	announced
⏵ 2	2018-12-04 04:07:58	announced	Updated project metadata.

Fornasiero EF, Mandad S, Wildhagen H, Alevra M, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Sakib MS, Fard MK, Kirli K, Centeno TP, Vidal RO, Rahman RU, Benito E, Fischer A, Dennerlein S, Rehling P, Feussner I, Bonn S, Simons M, Urlaub H, Rizzoli SO, Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions. Nat Commun, 9(1):4230(2018) [pubmed]

ProteomeXchange project tag: Human Brain Proteome Project (HUPO_HBPP) (B/D-HPP)

curator keyword: Biological

submitter keyword: Protein lifetimes, metabolic labeling, brain turnover, ELLPs, neuron, glia, cortex, cerebellum

Silvio O. Rizzoli
contact affiliation	Department of Neuro- and Sensory Physiology University Medical Center Göttingen Humboldtallee 23 37073 Göttingen
contact email	srizzol@gwdg.de
lab head
Sunit Mandad
contact affiliation	University Medical Centre Göttingen, Georg-August-Universität
contact email	smandad@gwdg.de
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/2018/11/PXD010859

PRIDE project URI

• PRIDE
  1. PXD010859
     1. Label: PRIDE project
     2. Name: Precisely measured protein lifetimes in the mouse