PXD000149-1

PXD000149 is an original dataset announced via ProteomeXchange.

Title	The potato tuber mitochondrial proteome
Description	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.
HostingRepository	PRIDE
AnnounceDate	2014-01-29
AnnouncementXML	Submission_2014-01-29_07:53:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jay J Thelen
SpeciesList	scientific name: Solanum tuberosum (Potato); NCBI TaxID: 4113;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-18 02:20:15	ID requested
⏵ 1	2014-01-29 07:53:09	announced
2	2014-07-25 00:53:41	announced	Updated project metadata.

Salvato F, Havelund JF, Chen M, Rao RS, Rogowska-Wrzesinska A, Jensen ON, Gang DR, Thelen JJ, M, ø, ller IM, The potato tuber mitochondrial proteome. Plant Physiol, 164(2):637-53(2014) [pubmed]

submitter keyword: potato

mitochondria

proteome

Solanum tuberosum

Jay J Thelen
contact affiliation	University of Missouri
contact email	thelenj@missouri.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/01/PXD000149

PRIDE project URI

• PRIDE
  1. PXD000149
     1. Label: PRIDE project
     2. Name: The potato tuber mitochondrial proteome