PXD010446

PXD010446 is an original dataset announced via ProteomeXchange.

Title	Sequential Fractionation Strategy Identifies Nine Missing Proteins in The Mitochondrial Proteome of Commonly Used Cell Lines
Description	Identification of mitochondrial proteins with a bottom up approach after organelle enrichment and 1D PAGE separation for 5 different cell lines. The bands were cut and the proteins reduced, alkylated and digested with trypsin according to a conventional protocol. Acquisition were performed on the Orbitrap Fusion Tribrid mass spectrometer in top speed mode with 3 seconds cycles. Raw data were processed using PEAKS Studio 7.5 (Bioinformatics Solutions Inc.) and searched using the PEAKS search engine and the SPIDER peptide mutation and homology search tool against neXtProt (July 2017; 42,151 total entries). Parent Mass Error Tolerance was set to 10.0 ppm and Fragment Mass Error Tolerance to 0.6 Da. Other search parameters were trypsin enzyme specificity, two missed cleavages per peptide, fixed Carbamidomethylation of Cys and variable Oxidation of Met, Deamidation of Gln and Asn (NQ), Phosphorylation of Ser, Thr and Tyr and Acetylation of Lys with two variable PTM per peptide. Non-specific cleavage was allowed to only one end of the peptide. FDR estimation was enabled, and precursor options corrected. To follow the HPP Mass Spectrometry Data Interpretation Guidelines Version 2.1 and in view of our goal of finding missing proteins, we set the FDR threshold on PSMs to 2%, typically resulting in FDR on peptides lower than 5% and we filtered out all the proteins identified with only one peptide, resulting in a FDR at the protein level of 0.0%.
HostingRepository	MassIVE
AnnounceDate	2018-10-12
AnnouncementXML	Submission_2018-10-12_07:49:23.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	Carbamidomethyl; Oxidation; Deamidated; Phospho; Acetyl
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-16 09:04:23	ID requested
⏵ 1	2018-10-12 07:49:24	announced

Ronci M, Pieroni L, Greco V, Scotti L, Marini F, Carregari VC, Cunsolo V, Foti S, Aceto A, Urbani A, Sequential Fractionation Strategy Identifies Three Missing Proteins in the Mitochondrial Proteome of Commonly Used Cell Lines. J Proteome Res, 17(12):4307-4314(2018) [pubmed]

submitter keyword: mt-HPP, missing proteins, mitochondrial proteome, protein fractionation, high-density datasets

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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