Mass spectrometry software is used for data acquisition, analysis, or representation in mass spectrometry.
In protein mass spectrometry, tandem mass spectrometry (also known as MS/MS or MS<sup>2</sup>) experiments are used for protein/peptide identification. Peptide identification algorithms fall into two broad classes: database search and de novo search. The former search takes place against a database containing all amino acid sequences assumed to be present in the analyzed sample. In contrast, the latter infers peptide sequences without knowledge of genomic data.
De novo peptide sequencing algorithms are, in general, based on the approach proposed in Bartels et al. (1990).