On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. 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
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