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PXD022299

PXD022299 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleImproving the identification and coverage of plant transmembrane proteins in Medicago using bottom-up proteomics
DescriptionPlant transmembrane proteins (TMPs) are essential for normal cellular homeostasis, nutrient exchange and responses to environmental cues. Commonly used bottom-up proteomic approaches fail to identify a broad coverage of peptide fragments derived from TMPs. Here, we used mass spectrometry (MS) to compare the effectiveness of two solubilisation and protein cleavage methods to identify shoot-derived TMPs from the legume Medicago. We compared a urea solubilisation, trypsin Lys-C (UR-TLC) cleavage method to a formic acid solubilisation, cyanogen bromide and trypsin Lys-C (FA-CTLC) cleavage method. We assessed the effectiveness of these methods by (i) comparing total protein identifications, (ii) determining how many TMPs were identified, and (iii) defining how many peptides incorporate all, or part, of transmembrane domains (TMD) sequences. The results show that the FA-CTLC method identified nine-fold more TMDs, and enriched more TMPs than the UR-TLC method. FA-CTLC identified more TMPs, particularly transporters, whereas, UR-TLC preferentially identified TMPs with one TMD, particularly signalling proteins. The results suggest that combining plant membrane purification techniques with both the FA-CTLC and UR-TLC methods will achieve a more complete identification and coverage of TMPs.
HostingRepositoryPRIDE
AnnounceDate2020-12-02
AnnouncementXMLSubmission_2021-01-06_06:25:42.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHan-Chung Lee
SpeciesList scientific name: Medicago tuberculata; NCBI TaxID: 1867346;
ModificationListdeaminated residue; iodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-11-02 07:57:15ID requested
12020-12-01 23:32:09announced
22021-01-06 06:25:43announced2021-01-06: Updated publication reference for PubMed record(s): 33391307.
Publication List
Lee HC, Carroll A, Crossett B, Connolly A, Batarseh A, Djordjevic MA, Using Bottom-Up Proteomics. Front Plant Sci, 11():595726(2020) [pubmed]
Keyword List
submitter keyword: TMD, TMP
Contact List
Michael Djordjevic
contact affiliationANU, RSB
contact emailMichael.Djordjevic@anu.edu.au
lab head
Han-Chung Lee
contact affiliationResearch school of biology, The Australian National University
contact emailHan.Lee@anu.edu.au
dataset submitter
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Dataset FTP location
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Repository Record List
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