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PXD000340

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2014-07-25
  • AnnouncementXML: Submission_2014-07-25_01:22:14.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Dong-Wen Lv
  • Title: Brachypodium distachyon three leaf stage LC-MSMS
  • Description: Leaves of Brachypodium distachyon Bd21 were collected at three leaf stage. The total proteins were extracted and then phosphopeptides were enriched by using TiO2 microcolumns and phosphopeptides and their corresponding proteins were identified with LC-MS/MS and Maxquant software. In details, enriched phosphopeptides were separated on a self-packed C18 reverse phase column (75 μm I.D., 150 mm length) (Column Technology Inc., Fremont, CA), which directly connected the nano electrospray ion source to a LTQ-Orbitrap XL mass spectrometer. Pump flow was split to achieve a flow rate at 1 μL/min for sample loading and 300 nL/min for MS analysis. The mobile phases consisted of 0.1% FA (A) and 0.1% FA and 80% ACN (B). A five-step linear gradient of 5% to 30% B in 105 min, 35% to 90% B in 16 min, 90% B in 4 min, 90% to 2% B for 0.5 min and 2% B for 14.5 min was performed. The spray voltage was set to 2.0 kV and the temperature of the heated capillary was 240ºC. For data acquisition, a data-dependent top 10 MS/MS spectraper MS full scan in the Orbitrapanalyser was used. The raw files were processed with Maxquant (version 1.1.1.36) and searched against the NCBI Brachypodium protein database (26,035 entries in total) concatenated with a decoy of reversed sequences. The following parameters were used for database searches: cysteine carbamidomethylation was selected as a fixed modification; methionine oxidation, protein N-terminal acetylation, and phosphorylation on serine, threonine and tyrosine were selected as variable modifications. Up to two missing cleavage points were allowed. The precursor ion mass tolerances were 7 ppm, and fragment ion mass tolerance was 0.5 Da for MS/MS spectra.
  • SpeciesList: scientific name: Brachypodium distachyon (Purple false brome) (Trachynia distachya); NCBI TaxID: 15368;
  • ModificationList: phosphorylated residue; Carbamidomethyl
  • Instrument: LTQ Orbitrap

Dataset History

VersionDatetimeStatusChangeLog Entry
02013-07-12 08:44:24ID requested
12013-12-17 02:29:40announced
12013-12-17 02:33:03announced
12013-12-17 02:39:59announced
22014-07-25 01:22:15announcedUpdated project metadata.

Publication List

  1. Dataset with its publication pending

Keyword List

  1. submitter keyword: Brachypodium, leaf, LC-MSMS, phosphorylation

Contact List

    Dong-Wen Lv
    • contact affiliation: College of Life Sciences
    • contact email: dw.lv@hotmail.com
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
Repository Record List
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