Available software/services for each core technology

APAF employs commercially available and open source 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. If you wish to access and analyse your Mascot results you can do so at http://bio.proteome.org.au




Description and further links



  • PeakView
  • Skyline
  • PeakView is a SCIEX software which is compatible with all SCIEX mass spectrometers and enables quantitative reviewing of the LC/MS spectrum and execute data analysis
  • Skyline is a open-source Windows client program for analysing SRM and DDA spectrometer data


  • Sciex ProteinPilot
  • A Sciex software package for protein identification and quantitation


  • Proteome Discoverer
  • A Thermo Scientific software package for protein identification and quantitation

Gel Image Analysis

  • Nonlinear Dynamics Progenesis
  • The standard tool we use for gel image analysis

Protein Identification

  • Matrix Science Mascot Search Engine
  • Matrix Science Mascot Distiller
  • Thermo Scientific Proteome Discoverer
  • The GPM X! Tandem Search Engine
  • NCBI OMSSA Search Engine
  • Scaffold analysis packages
  • Peptide/Protein Search Engines

Pathway analysis

  • Ingenuity Pathway Analysis
  • IPA is a software package used for modelling and analysing biological pathways for a set of proteins