Dataset Information

Sequential Fractionation Strategy Identifies Nine Missing Proteins in The Mitochondrial Proteome of Commonly Used Cell Lines

ABSTRACT: 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%.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Maurizio Ronci

PROVIDER: MSV000082409 | MassIVE | Mon May 28 01:33:00 BST 2018

SECONDARY ACCESSION(S): PXD010446

REPOSITORIES: MassIVE

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Sequential Fractionation Strategy Identifies Three Missing Proteins in the Mitochondrial Proteome of Commonly Used Cell Lines.

Ronci Maurizio M Pieroni Luisa L Greco Viviana V Scotti Luca L Marini Federica F Carregari Victor C VC Cunsolo Vincenzo V Foti Salvatore S Aceto Antonio A Urbani Andrea A

Journal of proteome research 20181005 12

Mitochondria are undeniably the cell powerhouse, directly affecting cell survival and fate. Growing evidence suggest that mitochondrial protein repertoire affects metabolic activity and plays an important role in determining cell proliferation/differentiation or quiescence shift. Consequently, the bioenergetic status of a cell is associated with the quality and abundance of the mitochondrial populations and proteomes. Mitochondrial morphology changes in the development of different cellular func ...[more]

PMID: 30284448

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