PABST

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-	-- PABST overview	+	== PABST overview
	This page describes the Peptide Atlas Best SRM Transition tool or PABST, which is a Peptide Atlas functionality that uses		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		various sources of information to produce lists of peptides and (optionally) fragment ions for use in selected reaction
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	assays.		assays.
-	--- Best peptide selection	+	=== Best peptide selection

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Revision as of 18:26, 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, and finally
this information in loaded into the Peptide Atlas database and forms are provided to query and retrieve list of potential
assays.  

=== Best peptide selection