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PXD000054

PXD000054 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteogenomic analysis of Helicobacter pylori strain 26695
DescriptionDear Sir or Madam, we report an in-depth proteogenomics study of Helicobacter pylori strain 26695 and provide the supporting MS data via ProteomExchange. The study includes 2 biological replicates with 6 different datasets: G1: in-gel digestion with trypsin, replicate 1 G2: in-gel digestion with trypsin, replicate 2 T1: SEC fractionation of low molecular weight (LMW) proteins and subsequent trypsin digestion, replicate 1 T2: SEC fractionation of LMW proteins and subsequent trypsin digestion, replicate 2 A1: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 1 A2: SEC fractionation of LMW proteins and subsequent AspN digestion, replicate 2 L1: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 1 L2: SEC fractionation of LMW proteins and subsequent LysC digestion, replicate 2 In our proteogenomics approach, we could identify four previously missing protein annotations and were able to correct sequences of six protein coding regions. Furthermore we identified signal peptidase cleavage sites for 72 different proteins. MGFs were generated by Maxquant 1.1 [1] using recalibration of peptide parent masses. For PRIDE (http://www.ebi.ac.uk/pride) submission, we made an additional database search with Mascot and X!Tandem using the SearchGUI [2]. Therefore we searched against a NCBI database of H. pylori strain 26695 complemented with the sequence corrections, signal peptide cleavage sites and missing annotations with the same configurations as described in materials and methods. For pride xml export we used the software PeptideShaker (http://code.google.com/p/peptide-shaker/). The complemented database has entries which will be submitted to the UniProtKB via SPIN. The entries have the according SPIN number as accession number. The NCBI accession numbers for the shortened sequences due to signal peptide cleavage are extended with “_1”. The fasta database is added to the submission. For additional information, please contact me: stephan.mueller@ufz.de Yours sincerely, Stephan Mueller References: [1] Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. Journal of proteome research. 2011;10:1794-805. [2] Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L. SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics. 2011;11:996-9.
HostingRepositoryPRIDE
AnnounceDate2017-10-24
AnnouncementXMLSubmission_2017-10-24_00:12:57.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000054
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterStephan Müller
SpeciesList scientific name: Helicobacter pylori 26695; NCBI TaxID: 85962;
ModificationListacetylated residue: 42.010565; 2-pyrrolidone-5-carboxylic acid (Glu): -18.010565; 2-pyrrolidone-5-carboxylic acid (Gln): -17.026549; iodoacetamide derivatized amino-terminal residue: 57.021464; monohydroxylated lysine: 15.994915
Instrumentinstrument model: LTQ-Orbitrap; LTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02012-10-18 03:43:06ID requested
12013-08-01 04:51:42announced
12014-07-28 00:24:13announced
22013-08-01 09:21:12announcedAdd reference
22017-06-21 00:30:31announcedUpdated project metadata.
32017-10-24 00:12:58announcedUpdated project metadata.
Publication List
M, ü, ller SA, Findei, ß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S, Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics, 86():27-42(2013) [pubmed]
Keyword List
submitter keyword: Proteogenomics, Proteomics, Helicobacter pylori strain, Signal peptide, Coding sequence, LTQ Orbitrap
Contact List
Stephan Müller
contact affiliationProteomics
contact emailstephan.mueller@ufz.de
dataset submitter
Full Dataset Link List
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/2013/08/PXD000054
PRIDE project URI
Repository Record List
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