ĭatabase search algorithm released in 2011 by Protein Metrics Inc. Developed by Jürgen Cox and others at the Max Planck Institute of Biochemistry. Identification of co-fragmented peptides improves the number of identified peptides. This combination enables analysis of large datasets on a desktop computer. Andromeda can function independently or integrated into MaxQuant. 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. 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