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

Technology	Software	Description and further links
SWATH/SRM DIA	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
iTRAQ/SILAC	Sciex ProteinPilot	A Sciex software package for protein identification and quantitation
TMT	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

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