Mascot – Matrix Science – Commercially available
Proteome Discoverer™ Software – Thermo Scientific – Commercially available
Scaffold – Proteome Software – Commercially available
MaxQuant – Max Planck Institute of Biochemistry – Freely available
Perseus – Max Planck Institute of Biochemistry – Freely available
PEAKS Studio -Bioinformatics Solutions Inc – Commercial available
OpenMS – Max Planck Institute for Developmental Biology – Freely available
Galaxy server – Medical School // Aristotle University of Thessaloniki