Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 410038
Title A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana
Author(s) Vertommen, A.; Moller, A.; Cordewener, J.H.G.; Swennen, R.; Panis, B.; Finnie, C.; America, A.H.P.; Carpentier, S.C.
Source Journal of Proteomics 74 (2011)8. - ISSN 1874-3919 - p. 1218 - 1229.
Department(s) PRI BIOS Applied Genomics & Proteomics
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) driven proteomics - lc-ms/ms - proteins - identification - organisms - system
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.
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