New. Analyse your Mascot proteomic results further http://bio.proteome.org.au
APAF employs commercially available and in-house built state-of-the-art bioinformatics tools for analysing proteomics data. We have terabytes of storage space for the vast amount of data that proteomics experiments generate.
For analysing iTRAQ/SILAC data, we use:
For gel image analysis, we use:
- Nonlinear Dynamics Progenesis
- Bio-Rad PDQuest
For protein identification we have the following in-house search engines:
- Matrix Science Mascot Search Engine
- Thermo Scientific Sequest Search Engine and BioWorks Browser
- The GPM Organisation X! Tandem Search Engine
- NCBI OMSSA Search Engine
NEW. Gene ontology annotation package: PloGO - an R package for summarizing gene ontology annotation and abundance
PloGO is a simple open source R package for plotting gene ontology annotation in a manner similar to other gene ontology plotting tools (e.g. Wego). However it was designed to incorporate information about abundance in addition to annotation, to handle multiple files and to allow for a targeted collection of categories of interest. PloGO was motivated by the analysis of multi-condition label free proteomics experiments, and relies on functionality provided by the GOstats and biomaRt R packages. Now accepted 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 (R version 2.12) bioinformatics package with the documentation. This is a zip file. A newer version is now available of PloGO (R version 2.14)
We also link to the ExPASy Proteomics Server.