1. D E F A B C D E F FeatureExplanation AcvParam indicating that peptide-level scoring has been done and that feature B MAY be present and features D, E and F MUST be present BThe threshold used to determine whether each distinct peptides group has been confidently identified – used to set the value of feature F CAs for regular mzIdentML files, a threshold can be applied at the level of PSMs – which is used to set the passThreshold attribute on DIf feature A is present, exactly one cvParam out of a set of several options MUST be present (if feature A is present) to indicate the mechanism used to groups different PSMs into distinct peptide entities. The value slot contains a unique identifier (string) that MUST be given to all elements within the same distinct peptide group. There is no expectation that meaningful information SHOULD be conveyed by the value slot, but implementers MAY choose to use the peptide sequence or peptide sequence and a modification string (depending on the grouping mechanism) as the value. EA cvParam containing the peptide-level score used for ordering distinct peptide entities, which MUST be given to all elements within the same distinct peptide group with the same value. FIf feature A is present, every element MUST contain the “peptide passes threshold” cvParam with a Boolean value. All elements within the same distinct peptide group MUST have the same value.

2. KYYGNVVYYIGER KYYGNVVYYIGER --> FeatureExplanation AIf modification rescoring has been performed, this cvParam MUST be present. BA Threshold for modification localizations MAY be inserted into the CThe ambiguity with respect to modification location is present at the level of but rescored software SHOULD use the residues and location attribute to insert the most likely location for the modification – NOTE: This is still open to debate DIf feature A is present, every referencing a peptide with a variable modification MUST have a cvParam for the location score. The value slot takes the following format MOD_ORDER:SCORE:POSITION:PASS_THRESHOLD MOD_ORDER = element order in the referenced object SCORE = Score or statistical measure associated with the modification position POSITION = Position of the modification on the peptide (N-terminus = 0, C-terminus = peptide length + 1). If the score pertains to grouped positions, different positions MUST be separated by “|” PASS_THRESHOLD = true | false with regards to the threshold specified in Feature A. If no Threshold has been specified, this MUST always be true. EThe modification position rescoring software SHOULD NOT include additional equal or lower ranked elements referencing a different element with the same peptide sequence and the same set of modifications (but with different modification positions) i.e. the only expected mechanism for specifying modification position is the cvParam specified in Feature D. A.... B C D E

3. AAFTKQAADK AMYPPKEDR A B D E FeatureExplanation AIf a crosslinking search has been performed, this cvParam MUST be present. BIf a pair of crosslinked peptides has been identified, one peptide’s Modification element MUST be flagged as “crosslink donor” and one MUST be flagged as “crosslink receiver”. The export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order. The crosslink donor Modification element MUST have the attribute monoisotopicMassDelta = the mass gain from the crosslink reagent. The crosslink receiver peptide’s Modification element MUST have monoisotopicMassDelta = 0. CThe crosslink donor peptide’s Modification element MUST have a suitably sourced cvParam for the crosslink. The crosslink receiver peptide’s Modification element MUST not have a cvParam for the reagent. DIf a crosslinked pair of peptides has been identified, there MUST be two elements with the same rank value. Both MUST have the “Cross-linked Spectrum Identification Item” cvParam, and the value acts as a local identifier with the to group these two elements together. EIf the search engine applies a score to the paired identification, both elements MUST have the same cvParam capturing the value. The two elements MAY also have independent scores for the two chains. C B