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PXD000118

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2018-01-11
  • AnnouncementXML: Submission_2018-01-11_00:30:19.xml
  • DigitalObjectIdentifier: http://dx.doi.org/10.6019/PXD000118
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Supported dataset by repository
  • PrimarySubmitter: Ken Pendarvis
  • Title: Proteomic analysis of Mycoplasma hyopneumoniae virulent strain 232
  • Description: The experiment consists of M.hyp 232 cultures digests analyzed on two mass specs, LTQ Velos Pro and LTQ FT Ultra LTQ Velos Pro: Six cell culture replicates of M.hyo 232 were hydrophobically separated using tree detergents: Digitonin, Tween, and SDS. Each francion, including the insoluble pellet, was trypsin digested and then cleaned using an SCX trap follwed by a RP trap to remove detergents. Each fraction was sepated using a Dionex U3000 splitless nanoflow system operating at 333 nl per minute using a gradient of 2% ACN to 50% ACN in 4 hours. Eluate was analyzed using an LTQ Velos Pro mass spectrometer with 20 MS/MS scans of the 20 most intense peaks from each MS scan. Dynamic exclusion was enable for 3 minutes for each m/z with a repeat count of 1. LTQ FT Ultra: Two cell pellets for high resolution analysis were lysed and trypsin digested. Digested peptides were dried, resuspended in 20 mM KH2PO4, 20% ACN, pH 3 (Buffer A) in 2.5 L and transferred to low retention vials in preparation for separation using an Ultimate 3000 configured for 2D-LC. Each sample was loaded at 15 l/min onto an SCX microtrap for the first dimension of separation, involving SCX steps of Buffer A + 0, 5, 10, 15, 20, 25, 30, 40, 50, 100, 250, 500, and 1000 mM KCl. For the second dimension of separation, each eluted salt step was desalted with an inline peptide microtrap with 2% ACN, 0.1% FA at 5 l/min. Once desalted, the microtrap was switched into line with a fritless nano column (75m x ~10cm) containing C18 media (5, 200 Magic, Michrom). Peptides were eluted using a gradient of 2% to 36% ACN, 0.1% FA at 350 nl/min over 60 min and electrospray ionized for analysis using an LTQ FT Ultra mass spectrometer. A survey scan m/z 350-1750 was acquired in the FT ICR cell (Resolution = 100,000 at m/z 400, with an accumulation target value of 1,000,000 ions). Up to the 6 most abundant ions (>3,000 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 seconds. Analysis: X!tandem searches were performed using the Mycoplasma hyopneumoniae strain 232 reference protein set from NCBI. The only difference between the searches for the LTQ Velos and LTQ FT was the precursor mass tolenance being set to +-1500ppm and +-24ppm respectively. Decoy searches were performed and the data filtered at e-value <= 0.01 with single peptide proteins discarded. These results are included in the submission as two tab-delimited text files.
  • SpeciesList: scientific name: Mycoplasma hyopneumoniae (strain 232); NCBI TaxID: 295358;
  • ModificationList: dihydroxylated residue; dehydrated residue; phosphorylated residue; deaminated residue; acetylated residue; iodoacetamide derivatized residue
  • Instrument: instrument model: LTQ FT Ultra; LTQ FT Ultra; LTQ Orbitrap Velos; instrument model: LTQ Velos Pro

Dataset History

VersionDatetimeStatusChangeLog Entry
02013-01-04 03:32:07ID requested
12018-01-10 05:30:08announced
22018-01-11 00:30:20announcedUpdated project metadata.

Publication List

  1. Pendarvis K, Padula MP, Tacchi JL, Petersen AC, Djordjevic SP, Burgess SC, Minion FC, Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232. BMC Genomics, 15():576(2014) [pubmed]

Keyword List

  1. curator keyword: Biomedical
  2. submitter keyword: Mycoplasma hyopneumoniae 232 LTQ Velos FT mass spec proteomics

Contact List

    Ken Pendarvis
    • contact affiliation: University of Arizona
    • contact email: jkpendarvis@email.arizona.edu
    • lab head:
    Ken Pendarvis
    • contact affiliation: Veterinary Science and Microbiology
    • contact email: jkpendarvis@email.arizona.edu
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
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