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PXD000340

PXD000340 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBrachypodium distachyon three leaf stage LC-MSMS
DescriptionLeaves 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.
HostingRepositoryPRIDE
AnnounceDate2014-07-25
AnnouncementXMLSubmission_2014-07-25_01:22:14.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterDong-Wen Lv
SpeciesList scientific name: Brachypodium distachyon (Purple false brome) (Trachynia distachya); NCBI TaxID: 15368;
ModificationListphosphorylated residue; Carbamidomethyl
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog 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
Dataset with its publication pending
Keyword List
submitter keyword: Brachypodium, leaf, LC-MSMS, phosphorylation
Contact List
Dong-Wen Lv
contact affiliationCollege of Life Sciences
contact emaildw.lv@hotmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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