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PXD007053 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleStandardization of mitochondrial proteomics v2 NP
DescriptionComparison 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 50 mM ammonium bicarbonate. Before digestion the proteins were first quantified according to the Bradford assay and then reduced with 1 mM TCEP 50 mM and alkylated wit IAA 20 mM. 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 - depending on the instrument - 10.0 to 40 ppm Fragment Mass Error Tolerance - depending on the instrument - 0.05 to 0.6 Da Enzyme specificity Trypsin Max Missed Cleavages: 2 Non-specific Cleavage: 1 Fixed Modifications: Carbamidomethylation (C) Variable Modifications: Oxidation (M), Deamidation (NQ) Max variable PTM per peptide: 2 The searched database was downloaded from www.nextprot.org and contained the latest annotated human proteome including isoforms (42,151 entries).
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterMaurizio Ronci
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListdeamidated L-asparagine; deamidated L-glutamine; L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine
InstrumentmaXis 4G; impact; Synapt G2-S HDMS; TripleTOF 5600; LTQ Orbitrap Velos; Orbitrap Fusion; LTQ Orbitrap XL
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-07-14 07:47:49ID requested
12017-09-18 12:15:15announced
Publication List
Alberio T, Pieroni L, Ronci M, Banfi C, Bongarzone I, Bottoni P, Brioschi M, Caterino M, Chinello C, Cormio A, Cozzolino F, Cunsolo V, Fontana S, Garavaglia B, Giusti L, Greco V, Lucacchini A, Maffioli E, Magni F, Monteleone F, Monti M, Monti V, Musicco C, Petrosillo G, Porcelli V, Saletti R, Scatena R, Soggiu A, Tedeschi G, Zilocchi M, Roncada P, Urbani A, Fasano M, Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative. J Proteome Res, 16(12):4319-4329(2017) [pubmed]
Keyword List
submitter keyword: Mt-HPP, Mitochondria enrichment protocol, human cell lines, orbitrap, qtof, high resolution
Contact List
Maurizio Ronci
contact affiliationUniversity G. d'Annunzio
contact emailmaurizio.ronci@unich.it
lab head
Maurizio Ronci
contact affiliationUniversity G. d'Annunzio
contact emailmaurizio.ronci@unich.it
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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