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PXD001852

PXD001852 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProtein gel band method for improving the identification of stem proteins
DescriptionIdentifying the intracellular and cell wall-ionically bound glycoside hydrolases (GHs) carbohydrate esterases (CEs) at the late growth stage of Arabidopsis stems is important for understanding the mechanisms regulating the cell wall integrity. The fact that whole plant stems are used as biomass feedstocks and the mixing of intracellular proteins with the cell wall proteome caused by an increasing proportion of broken cells of stems at the late growth stage pose a challenge in identifying these GHs and CEs. Here, we used a CaCl2-extraction procedure to isolate non-structural proteins from Arabidopsis whole stems, followed by protein solution method for direct identification of stem proteins, and by SDS-PAGE separation and protein gel band method for improving the identification of stem proteins, using Nano-LC-MS/MS analysis. Totally, 75 and 236 stem proteins were identified by using these two methods, respectively, confirming the later method (i.e. protein gel method) identified three time more stem proteins. Among these proteins, based on cell wall protein databases and data mining analyses, 6 and 22 proteins were identified as cell wall proteins from the late growth stage Arabidopsis stems, by using these two methods respectively.
HostingRepositoryPRIDE
AnnounceDate2015-05-11
AnnouncementXMLSubmission_2015-05-11_08:55:07.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterShihui Yang
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationListNo PTMs are included in the dataset
InstrumentLCQ Classic
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-02-27 06:50:27ID requested
12015-05-11 08:55:08announced
Publication List
Dataset with its publication pending
Keyword List
curator keyword: Technical
submitter keyword: cell wall proteins, glycoside hydrolase, xylan-modifying enzyme, pectin-modifying enzyme, plant late growth stage, plant senescence, biomass recalcitrance, feedstock engineering
Contact List
Hui Wei
contact affiliationNREL
contact emailHui.Wei@nrel.gov
lab head
Shihui Yang
contact affiliationNational Renewable Energy Lab
contact emailshihui.yang@nrel.gov
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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