Dataset Information

The potato tuber mitochondrial proteome

ABSTRACT: The potato tuber mitochondrial proteome Three biological replicates, 40 gel sections each (120 files) MS raw files (.raw) and peptide search files [MASCOT (.msf), MSGFBD (.txt), PROLUCID (.sqt) and SEQUEST (_sequest.msf)] Mitochondria were isolated from dormant potato tubers (Solanum tuberosum) and proteins (0.25 mg) resolved by one-dimensional gel electrophoresis , sectioned into 40 equal segments, and tryptic peptides analyzed by liquid chromatography tandem mass spectrometry using an Orbitrap XL. Acquired MS/MS spectra were searched using different algorithms against the potato protein database (http://www.potatogenome.net). To estimate the protein false discovery rate (FDR), randomized sequences were combined with the forward database in a concatenate format. MASCOT server 2.3.01, SEQUEST, MS-GFDB and ProLuCID software were used to interpret the data set using very similar parameters. MASCOT and SEQUEST were used integrated within Proteome Discoverer 1.3 software package (Thermo Scientific). Raw files (Thermo) were converted to ms2 and mzXML files to run ProLuCID and MS-GFDB softwares. All search engines were configured to the following parameters: MW range between 200 and 2,000; 1,000 ppm of precursor ion tolerance; oxidation of methionine and asparagine deamidation as variable modifications and carbamidomethylation of cysteine as a static modification; trypsin; 2 allowed missed cleavages. After searches, the PSMs were filtered out at 5ppm of precursor ion tolerance achieving a false discovery rate (FDR) lower than 1% at the protein level for each biological replicate. Filtered data were uploaded on Protein Herder module within Compass package for protein grouping. At this step, all sets of indistinguishable proteins, which were assigned by the same peptides, are combined into protein groups.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Solanum Tuberosum (potato)

SUBMITTER: RSP RAO

PROVIDER: PXD000149 | Pride | 2014-01-28

REPOSITORIES: pride

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The potato tuber mitochondrial proteome.

Salvato Fernanda F Havelund Jesper F JF Chen Mingjie M Rao R Shyama Prasad RS Rogowska-Wrzesinska Adelina A Jensen Ole N ON Gang David R DR Thelen Jay J JJ Møller Ian Max IM

Plant physiology 20131218 2

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using fou ...[more]

PMID: 24351685

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			Action	DRS
	Ob07720.msf	Msf
	Ob07720.mzXML.txt	Mzxml
	Ob07720.raw	Raw
	Ob07720.sqt	Other
	Ob07720_sequest.msf	Msf