PXD000149 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2014-07-25 |
AnnouncementXML | Submission_2014-07-25_00:53:41.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 |
Dataset History
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. |
Publication List
Salvato F, Havelund JF, Chen M, Rao RS, Rogowska-Wrzesinska A, Jensen ON, Gang DR, Thelen JJ, M, ΓΈ, ller IM, The potato tuber mitochondrial proteome. Plant Physiol, 164(2):637-53(2014) [pubmed] |
Keyword List
submitter keyword: potato |
mitochondria |
proteome |
Solanum tuberosum |
Contact List
Jay J Thelen |
contact affiliation | University of Missouri |
contact email | thelenj@missouri.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000149
- Label: PRIDE project
- Name: The potato tuber mitochondrial proteome