Peptidomics Methods and Protocols
Despite being known and studied for years, peptides have never before attracted enough attention to necessitate the invention of the term "peptidomics" in order to specify the study of the complement of peptides from a cell, organelle, tissue or organism.
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1. Introduction Plant peptides can be defined as small proteins, below an arbitrary molecular weight or length cut-off (1). Peptides can be generated either from a gene encoding a small open reading frame, or they can be produced from a larger protein that undergoes posttranslational proteolytic cleavages that give rise to one or more smaller peptides. Proteolytically produced peptides may be bioactive functional peptides or they may represent non-functional turnover of formerly active proteins. The cleavage sites of plant M. Soloviev (ed.), Peptidomics, Methods in Molecular Biology 615, DOI 10.1007/978-1-60761-535-4 26, © Humana Press, a part of Springer Science+Business Media, LLC 2010
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proteolytic enzymes are not well established, so it is not possible to look at primary amino acid sequences and identify which proteins will be processed or which mature peptides will result. Nine plant signalling peptides have been intensively characterized by biochemical and molecular genetic experiments (2–13). These founding peptides coupled with the availability of genome sequences have led to the identification of additional peptides through bioinformatics analyses (9, 10, 14–18). In addition, based on the collective properties of identified plant peptides, some general properties have emerged. This information has been exploited to find additional peptides (19). The purpose of this review is to suggest how to use available tools and resources with the goal of identifying plant peptides of interest for further investigation. BLAST (20, 21) is a useful and well-known bioinformatic tool that can be used to find additional members of a gene family, if a founding member is available to use as a query. For example, many plant peptides that were originally identified through genetic or biochemical studies were found to belong to families of genes encoding similar peptides (9, 15). Using BLAST with default settings is not ideal for plant peptide studies. Various parameters involved in BLAST searches will be discussed as well as the rationale for changing them. The overall goal of the specific parameters suggested is to increase sensitivity. Following these changes, one will greatly increase the odds of finding meaningful similar sequences in the database when searching with short queries. At the same time spurious matches will increase, so healthy scepticism, sound judgement and further investigation will be required.
2. Materials 1. A personal computer with a web browser installed and Internet access are required. 2. TAIR BLAST at The Arabidopsis Information Resource (http://www.arabidopsis.org/Blast). 3. SignalP3.0 (http://www.cbs.dtu.dk/services/SignalP). 4. TMHMM2.0 (http://www.cbs.dtu.dk/services/TMHMM). 5a. TAIR bulk data retrieval and analysis tools (http://www. arabidopsis.org/tools/bulk/index.jsp). 5b. TAIR bulk protein search page (http://www. arabidopsis.org/tools/bulk/protein/index.jsp).
Plant Peptides Bioinfomatics
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5c. TAIR gene description search and download page (http://www.arab
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