PXD000094

PXD000094 is an original dataset announced via ProteomeXchange.

Title	Proteogenomics of Tistlia consotensis
Description	Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions.Peak lists were generated with the MASCOT DAEMON software (version 2.3.2) from Matrix Science using the extract_msn.exe data import filter from the Xcalibur FT package (version 2.0.7) proposed by ThermoFisher. Data import filter options were set at 400 (minimum mass), 5,000 (maximum mass), 0 (grouping tolerance), 0 (intermediate scans), and 1,000 (threshold). MS/MS spectra were searched against the  home-made ORF database with the following parameters: tryptic peptides with a maximum of 2 miss cleavages during proteolytic digestion, a mass tolerance of 5 ppm on the parent ion and 0.5 Da on the MS/MS, fixed modification for carbamidomethylated Cys (+57.0215) and variable modification for oxidized Met (+15.9949).  All peptide matches with a peptide score above its query threshold set at p < 0.05 with the ORF database and rank 1 were parsed using the IRMa 1.28.0 software. False-positive rate for peptide identification was estimated using a decoy database as below 0.5% with these parameters. MS/MS spectra assigned to several loci were systematically removed. A protein was considered validated when at least two different peptides were detected in the same experiment. False-positive identification of proteins was estimated using a reverse decoy database as below 0.1% with these parameters The number of MS/MS spectra per protein (spectral counts) was determined for the three replicates in each growth condition. The protein abundances were compared using the T-Fold option of the PatternLab 2.0 software. This module allows normalising the spectral count datasets, calculating the average fold changes with statistics (t-test), and estimating the resulting theoretical false discovery rate. Stringent parameters were used in this analysis: minimum fold change of 1.5, minimum p-value of 0.05 and BH-FDR Alfa of 0.15.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:26:34.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000094
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jean ARMENGAUD
SpeciesList	scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2012-12-11 03:01:48	ID requested
1	2012-12-18 03:05:23	announced
1	2014-05-21 06:33:37	announced
⏵ 2	2014-07-28 00:26:35	announced	Updated project metadata.

Rubiano-Labrador C, Bland C, Miotello G, Gu, é, rin P, Pible O, Baena S, Armengaud J, Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring. J Proteomics, 97():36-47(2014) [pubmed]

submitter keyword: Proteogenomics, Draft genome, Halotolerance, Alphaproteobacteria, Rhodospirillaceae

Jean ARMENGAUD
contact affiliation	CEA-DSV-iBEB-SBTN-LBSP
contact email	jean.armengaud@cea.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000094
     1. Label: PRIDE project
     2. Name: Proteogenomics of Tistlia consotensis