PXD000504

PXD000504 is an original dataset announced via ProteomeXchange.

Title	Campylobacter concisus strain BAA-1547 GeLC-MSMS
Description	Bacteria were washed 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
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_03:50:21.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000504
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	A Tay
SpeciesList	scientific name: Campylobacter concisus (strain 13826); NCBI TaxID: 360104;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: ESI-TRAP

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-09 02:05:22	ID requested
1	2014-04-28 06:48:38	announced
⏵ 2	2014-07-24 03:50:22	announced	Updated project metadata.

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]

curator keyword: Biological

submitter keyword: Campylobacter, concisus, GeLC-MSMS

A Tay
contact affiliation	School of Biotechnology and Biomolecular Sciences
contact email	aidan.tay@unsw.edu.au
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/2014/04/PXD000504

PRIDE project URI

• PRIDE
  1. PXD000504
     1. Label: PRIDE project
     2. Name: Campylobacter concisus strain BAA-1547 GeLC-MSMS