PXD006623

PXD006623 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Standardization of mitochondrial proteomics
Description	Comparison of the extraction performances of three different mitochondria enrichment protocols (differential centrifugation, sucrose gradient, a commercial kit based on surfactants) on ten different cell lines. Samples were analysed on several instrumental platforms. Mitochondrial pellets were lysed in RapiGest 0.1% (RG, Waters Corporation) and digested with trypsin in 50mM ammonium bicarbonate. Before digestion the proteins were first quantified according to the Bradford assay and then reduced with 1mM TCEP 50 mM and alkylated wit IAA 20mM. Peptides were recovered by centrifugation and then loaded directly on the respective chromatographic system for the mass spectrometry analysis or on a SDS-PAGE for WB analysis. Raw data were processed with PEAKS 7.5 with the following search parameters: Parent Mass Error Tolerance: 10.0 ppm; Fragment Mass Error Tolerance: 0.05 Da; Enzyme specificity: Trypsin; Max Missed Cleavages: 2; Non-specific Cleavage: one; Fixed Modifications: Carbamidomethylation (C); Variable Modifications: Oxidation (M), Acetylation (K) Ubiquitin; Deamidation (NQ); Max variable PTM per peptide: 2. The database searched was custom made and contained Uniprot Swiss Prot Human, common contaminants and yeast enolase (20442 entries).
HostingRepository	MassIVE
AnnounceDate	2018-02-28
AnnouncementXML	Submission_2018-02-28_04:43:31.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maurizio Ronci
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Deamidated
Instrument	maXis 4G; impact; Synapt G2-S HDMS; TripleTOF 5600; LTQ Orbitrap Velos; Orbitrap Fusion; LTQ Orbitrap XL

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-30 04:44:57	ID requested
⏵ 1	2018-02-28 04:43:31	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Mt-HPP, Mitochondria enrichment protocol, human cell lines, orbitrap, qtof, high resolution

submitter keyword: Mt-HPP, Mitochondria enrichment protocol, human cell lines, orbitrap, qtof, high resolution

Contact List

Maurizio Ronci
contact affiliation	University G. d'Annunzio
contact email	maurizio.ronci@unich.it
lab head
Maurizio Ronci
contact affiliation	University G. d'Annunzio
contact email	maurizio.ronci@unich.it
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/MSV000081121

MassIVE dataset URI

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://massive.ucsd.edu/MSV000081121