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

Publication: Research - peer-reviewJournal article – Annual report year: 2011

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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
JournalJournal of Proteomics
Publication date2011
Volume74
Issue8
Pages1218-1229
ISSN1874-3919
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 13

Keywords

  • MS Homology, Protein identification, Cytoscape, Poorly sequenced plants, Plasma membrane proteomics
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