PXD022299

PXD022299 is an original dataset announced via ProteomeXchange.

Title	Improving the identification and coverage of plant transmembrane proteins in Medicago using bottom-up proteomics
Description	Plant 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.
HostingRepository	PRIDE
AnnounceDate	2020-12-02
AnnouncementXML	Submission_2021-01-06_06:25:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Han-Chung Lee
SpeciesList	scientific name: Medicago tuberculata; NCBI TaxID: 1867346;
ModificationList	deaminated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-02 07:57:15	ID requested
1	2020-12-01 23:32:09	announced
⏵ 2	2021-01-06 06:25:43	announced	2021-01-06: Updated publication reference for PubMed record(s): 33391307.

Lee HC, Carroll A, Crossett B, Connolly A, Batarseh A, Djordjevic MA, Using Bottom-Up Proteomics. Front Plant Sci, 11():595726(2020) [pubmed]

submitter keyword: TMD, TMP

Michael Djordjevic
contact affiliation	ANU, RSB
contact email	Michael.Djordjevic@anu.edu.au
lab head
Han-Chung Lee
contact affiliation	Research school of biology, The Australian National University
contact email	Han.Lee@anu.edu.au
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD022299

PRIDE project URI

• PRIDE
  1. PXD022299
     1. Label: PRIDE project
     2. Name: Improving the identification and coverage of plant transmembrane proteins in Medicago using bottom-up proteomics