Table II. New CV terms in the PSI-MS CV that are now mandatory within the element <SpectrumIdentificationProtocol>, enabling the new features in mzIdentML 1.2 to be differentiated and recognized automatically by processing software. In the file, 1 … n of the terms MUST be present.

CV term name	Accession number	Comments/Purpose
Peptide-level scoring	MS:1002490	Statistics have been performed on non-redundant peptide identifications.
Modification localization scoring	MS:1002491	Scoring has been performed on the sites of peptide modification.
Consensus scoring	MS:1002492	Multiple search engines have been used for peptide identification.
Sample prefractionation	MS:1002493	The file contains the results of merged pre-fractionation analyses.
Cross-linking search	MS:1002494	The search engine has analysed cross-linked (and regular) peptides, using the new encoding described here.
De novo search	MS:1001010	De novo sequencing of peptides has been performed, meaning that 0 . . n relationships from peptides to proteins are allowed (rather than 1 . . n).
Proteogenomics search	MS:1002635	Peptides have been mapped back to genome level coordinates, stored in the file.
Spectral library search	MS:1001031	The identifications have been made by searching against a spectral library. 0 . . n peptides to proteins are allowed (rather than 1 . . n elsewhere) for cases where peptide to protein relationships are unknown in the library, or where a library entry has been identified with no known peptide sequence.
No special processing	MS:1002495	Used to indicate that none of the above features have been included in the file.