Table 1.

New CV terms for reporting protein set (group) relationships and global statistics about the protein identification results. The semantic validation software for mzIdentML (v.1.2) reports an error (MUST), a warning (SHOULD) or an informational message (MAY) if these terms are not reported within the file.

mzIdentML context	CV term	Values	Requirement level	Description
ProteinDetectionList	count of identified proteins	xsd:integer	MUST	The value reported MUST equal the number of PAGs with “protein group passes threshold” value = “true”
ProteinDetectionList	count of identified clusters	xsd:integer	MAY	If protein clusters have been reported in the file, the exporter may choose to annotate the ProteinDetectionList with the number identified above threshold.
ProteinAmbiguity-Group	number of distinct protein sequences	xsd:integer	MAY	The number of distinct protein sequences among the PDHs in the group. For example, if there are two PDHs with different identifiers that have identical full length sequences, the value would be 1.
ProteinAmbiguity-Group	cluster identifier	xsd:integer	MAY	An identifier applied to protein groups to indicate that they are linked by shared peptides.
ProteinDetection-Hypothesis	leading protein OR non-leading protein	-	MUST OR MUST	Every PDH in each PAG MUST be flagged as a leading protein or a non-leading protein and each PAG MUST contain at least one leading protein, but MAY contain more than one. A “leading protein” is defined as a protein that has the strongest or near strongest (further explained in Table 2) set of evidence for being present in the sample studied, amongst the grouped protein accessions. A “non-leading protein” is defined as a protein that has (substantially) less evidence than other proteins within the same group, and is thus less likely to have been present in the sample studied.
ProteinDetection-Hypothesis	group representative	-	MAY	Each PAG MAY contain zero or one PDH flagged as the group representative, if the software wishes to flag a preference (often arbitrary or for example based on alphabetical ordering) amongst the leading proteins. The group representative term can thus be viewed a “tiebreaker” if the export software wishes to make this distinction.
ProteinDetection-Hypothesis	Sequence Same-Set Protein	xsd: “list_of_strings” space separated list of PDH IDs that are same-set.	MAY	A protein that is indistinguishable or equivalent to another protein in the group, having matches to an identical set of peptide sequences.
ProteinDetection-Hypothesis	Spectrum Same-Set Protein	xsd: “list_of_strings” space separated list of PDH IDs that are same-set.	MAY	A protein that is indistinguishable or equivalent to another protein in the group, having PSMs derived from the same set of spectra.
ProteinDetection-Hypothesis	Sequence Subset Protein	xsd: “list_of_strings” space separated list of PDH IDs that are super-set.	MAY	A protein for which the matched peptide sequences are a subset of the matched peptide sequences for another protein in the group.
ProteinDetection-Hypothesis	Spectrum Subset Protein	xsd: “list_of_strings” space separated list of PDH IDs that are super-set.	MAY	A protein for which the matched spectra are a subset of the matched spectra for another protein in the group.
ProteinDetection-Hypothesis	Sequence Multiply Subsumable Protein	xsd: “list_of_strings” space separated list of PDH IDs that subsume this PDH.	MAY	A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group.
ProteinDetection-Hypothesis	Spectrum Multiply Subsumable Protein	xsd: “list_of_strings” space separated list of PDH IDs that subsume this PDH.	MAY	A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group.
ProteinDetection-Hypothesis	Marginally distinguished protein	-	MAY	Assigned to a non-leading PDH that has some independent evidence to support its presence relative to the leading protein(s) e.g. the PDH may have a unique peptide but not sufficient to be promoted as, for example, a leading protein of another a PAG.