SWATHXtend - (NEW) APAF developed software to extend peptide assay libraries for improved SWATH analysis
iTRAQ typical output from a std analysis - iTRAQ requires some consultation with APAF staff for experimental design and here we show an example of the possibe results.
Analyse your Mascot proteomic results further http://bio.proteome.org.au
Gene ontology annotation package: PloGO - an R package for summarizing gene ontology annotation and abundance
PloGO is a simple open source R package forplotting gene ontology annotation in a manner similar to other geneontology plotting tools (e.g. Wego). However it was designed toincorporate information about abundance in addition to annotation, tohandle multiple files and to allow for a targeted collection ofcategories of interest. PloGO was motivated by the analysis ofmulti-condition label free proteomics experiments, and relies onfunctionality provided by the GOstats and biomaRt R packages. Nowaccepted for Publication.
PloGO: Plotting Gene Ontology annotation and abundance in multi-condition proteomics experiments Dana Pascovici, Tim Keighley, Mehdi Mirzaei, Paul A. Haynes and Brett Cooke (Proteomics technical brief –Accepted, Nov 2011)
Link here to get required PloGO (Rversion 2.12) bioinformatics package with the documentation. This is azip file. A newer version compatible with R (Version 3.0.1) is nowavailableis now available of PloGO< (PloGO version 2.0 R V3.0.1)
We also link to the ExPASy Proteomics Server.