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PXD000505

PXD000505 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCampylobacter concisus UNSWCD GeLC-MSMS
DescriptionWashed three times in NaCl (150 mM). Cells were resuspended in 1 ml TSU buffer (50 mM Tris pH 8.0, 0.1% SDS, 2.5 M urea) and lysed by two freeze-thaw cycles in liquid nitrogen. Lysate proteins (40 ug) were separated and digested. Digested peptides were separated by nano-LC using an Ultimate 3000 HPLC and autosampler system (Dionex; Amsterdam, Netherlands). Samples (1 ul) were concentrated and desalted onto a micro C18 pre-column (500 um×2 mm, Michrom Bioresources; Auburn, CA, USA) with H2O:CH3CN (98:2, 0.05% trifluoroacetic acid) at 15 ul min−1. After a 4 min wash the pre-column was switched (Valco 10 port valve; Dionex) into line with a fritless nano column (75 u×~10 cm) containing C18 media (5 u, 200 A Magic; Michrom) manufactured according to Gatlin. Peptides were eluted using a linear gradient of H2O:CH3CN (98:2, 0.1% formic acid) to H2O:CH3CN (64:36, 0.1% formic acid) at 250 nl min−1 over 30 min. High voltage (2000 V) was applied to low volume tee (Upchurch Scientific) and the column tip positioned ~0.5 cm from the heated capillary (T = 280 degrees C) of an Orbitrap Velos (Thermo Electron; Bremen, Germany) mass spectrometer. Positive ions were generated by electrospray and the Orbitrap operated in data dependent acquisition mode (DDA). A survey scan m/z 350–1750 was acquired in the Orbitrap (Resolution = 30,000 at m/z 400, with an accumulation target value of 1,000,000 ions) with lockmass enabled. Up to the 10 most abundant ions (>5,000 counts) with charge states >+2 were sequentially isolated and fragmented within the linear ion trap using collisionally induced dissociation with an activation q = 0.25 and activation time of 30 ms at a target value of 30,000 ions. M/z ratios selected for MS/MS were dynamically excluded for 30 s. Peak lists were generated using Mascot Daemon/extract_msn (Matrix Science, Thermo; London, England) using the default parameters, and submitted to the database search program Mascot (version 2.1, Matrix Science). Search parameters were: Precursor tolerance 4 ppm and product ion tolerances +/-0.4 Da Oxidation (M) and Carbamidomethyl (C) specified as variable modifications Enzyme specificity was trypsin, 1 missed cleavage was possible
HostingRepositoryPRIDE
AnnounceDate2014-07-24
AnnouncementXMLSubmission_2014-07-24_03:50:24.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000505
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterA Tay
SpeciesList scientific name: Campylobacter concisus UNSWCD; NCBI TaxID: 929793;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
Instrumentinstrument model: ESI-TRAP
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-10-09 02:42:15ID requested
12014-04-28 06:52:25announced
22014-07-24 03:50:24announcedUpdated project metadata.
Publication List
Pang CN, Tay AP, Aya C, Twine NA, Harkness L, Hart-Smith G, Chia SZ, Chen Z, Deshpande NP, Kaakoush NO, Mitchell HM, Kassem M, Wilkins MR, Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J Proteome Res, 13(1):84-98(2014) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Campylobacter, concisus, GeLC-MSMS
Contact List
A Tay
contact affiliationSchool of Biotechnology and Biomolecular Sciences
contact emailaidan.tay@unsw.edu.au
dataset submitter
Full Dataset Link List
Dataset FTP location
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