title: A workflow for peptide-based proteomics in a poorly sequenced plant: a case study on the plasma membrane proteome of banana.
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.
authors.affiliation: Laboratory of Tropical Crop Improvement, Department of Biosystems, K.U. Leuven, Kasteelpark Arenberg 13, PO box 2455, B-3001 Heverlee, Belgium.
authors.forename: A
authors.initials: A
authors.lastname: Vertommen
authors.forename: A L B
authors.initials: AL
authors.lastname: Møller
authors.forename: J H G
authors.initials: JH
authors.lastname: Cordewener
authors.forename: R
authors.initials: R
authors.lastname: Swennen
authors.forename: B
authors.initials: B
authors.lastname: Panis
authors.forename: C
authors.initials: C
authors.lastname: Finnie
authors.forename: A H P
authors.initials: AH
authors.lastname: America
authors.forename: S C
authors.initials: SC
authors.lastname: Carpentier
mesh_terms: D002462:Cell Membrane / Q000737:chemistry; D008565:Membrane Proteins / Q000235:genetics / Q000302:isolation & purification*; D028521:Musa / Q000737:chemistry; D010455:Peptides / Q000302:isolation & purification; D010940:Plant Proteins / Q000235:genetics / Q000302:isolation & purification*; D020543:Proteome / Q000235:genetics; D040901:Proteomics / Q000379:methods*
chemical_list: D008565:Membrane Proteins; D010455:Peptides; D010940:Plant Proteins; D020543:Proteome