• Bioinformatics at APAF

    The bioinformatics group was established to support researchers with their data analysis needs and to help them derive experimental insights from their proteomics results.  We provide software and tools to support the variety of services provided by the other APAF groups, and have in-depth experience with a variety of commercial and academic projects, with particular areas of strength being cytokine analysis, plant proteomics, and statistical and machine learning based approaches to the analysis of novel proteomics techniques such as SWATH, labelled isobaric techniques, cytokines and label free shotgun proteomics.  We have had recent commercial experience in the area of cancer diagnostic tests and agriculturally important plants disease, have participated in national collaborative cross-platform research initiatives, and have engaged in numerous research academic collaborations.

  • 1.  Available software and services by core technology
    2.  Software tools and workflows developed in-house    
    3.  Custom analyses services and case studies


  • 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

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.