Developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry. It can function independently or integrated into MaxQuant, enabling analysis of large datasets on a desktop computer. It can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample, whereas the latter infers peptide sequences without knowledge of genomic data.Īndromeda is a peptide search engine based on probabilistic scoring. Peptide identification algorithms fall into two broad classes: database search and de novo search. In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS 2) experiments are used for protein/ peptide identification.
Further information: protein mass spectrometry
