PABST

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	assays.		assays.
-	=== Best peptide selection ===	+	=== Peptide list selection ===
-	The 'best' peptide for a given application is often a very subjective decision,	+	The criteria for selecting the list of most suitable peptides from a target protein are primarily based on the likelihood of
		+	observation and the presence or absence of various sequence features. This is done by applying weighting factors which can
		+	be modified by editing the configuration file fed to the command line peptide selector. This is described in some detail on
		+	[http://tools.proteomecenter.org/wiki/index.php?title=PABST_peptide_examples [this page]]

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Revision as of 18:46, 28 September 2009

PABST overview

 This page describes the Peptide Atlas Best SRM Transition tool or PABST, which is a Peptide Atlas functionality that uses
various sources of information to produce lists of peptides and (optionally) fragment ions for use in selected reaction 
monitoring (SRM) assays.  This information is compiled into 'builds' that allow for fast querying via a web interface, 
which can be found at following URL:  https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPABSTList

 The PABST build process has 3 discrete steps which are described in more detail in the following paragraphs.  First of all,
a list of the the top N (currently 10) most suitable peptides is determined for each protein in the target organism.  
Secondly, a list of the top M (currently 8) potential fragment ions from each selected peptide is determined.  Finally
this information in loaded into the Peptide Atlas database and forms are provided to query and retrieve list of potential
assays.  

Peptide list selection

 The criteria for selecting the list of most suitable peptides from a target protein are primarily based on the likelihood of 

observation and the presence or absence of various sequence features. This is done by applying weighting factors which can be modified by editing the configuration file fed to the command line peptide selector. This is described in some detail on [this page]