PXD007053-1

PXD007053 is an original dataset announced via ProteomeXchange.

Title	Standardization of mitochondrial proteomics v2 NP
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 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).
HostingRepository	MassIVE
AnnounceDate	2017-09-18
AnnouncementXML	Submission_2017-09-18_12:15:13.xml
DigitalObjectIdentifier
ReviewLevel	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	deamidated L-asparagine; deamidated L-glutamine; L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine
Instrument	maXis 4G; impact; Synapt G2-S HDMS; TripleTOF 5600; LTQ Orbitrap Velos; Orbitrap Fusion; LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-14 07:47:49	ID requested
⏵ 1	2017-09-18 12:15:15	announced

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]

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

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

MassIVE dataset URI

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