A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana

A. Vertommen, A. Moller, J.H.G. Cordewener, R. Swennen, B. Panis, C. Finnie, A.H.P. America, S.C. Carpentier

    Research output: Contribution to journalArticleAcademicpeer-review

    29 Citations (Scopus)

    Abstract

    Membrane proteins are an interesting class of proteins because of their functional importance. Unfortunately their analysis is hampered by low abundance and poor solubility in aqueous media. Since shotgun methods are high-throughput and partly overcome these problems, they are preferred for membrane proteomics. However, their application in non-model plants demands special precautions to prevent false positive identification of proteins. In the current paper, a workflow for membrane proteomics in banana, a poorly sequenced plant, is proposed. The main steps of this workflow are (i) optimization of the peptide separation, (ii) performing de novo sequencing to allow a sequence homology search and (iii) visualization of identified peptide–protein associations using Cytoscape to remove redundancy and wrongly assigned peptides, based on species-specific information. By applying this workflow, integral plasma membrane proteins from banana leaves were successfully identified.
    Original languageEnglish
    Pages (from-to)1218-1229
    JournalJournal of Proteomics
    Volume74
    Issue number8
    DOIs
    Publication statusPublished - 2011

    Keywords

    • driven proteomics
    • lc-ms/ms
    • proteins
    • identification
    • organisms
    • system

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