Highlights of proposed changes 1. Re-name "anchor protein" to representative protein (or--clearer but more cumbersome--arbitrary representative protein as suggested by Matt Chambers) -- each is a representative from a group of indistinguishable proteins, and the word "anchor" seems to imply greater significance. 2. Add the term independent-evidence protein for representative proteins that are not sub-set or subsumable. This will help the consumer make use of same-set/subsumable information. 3. Re-name "family member protein" to "marginally distinguished protein", to avoid implying an actual family relationship. 4.. Add two new terms from Cedar: canonical protein: a set of independent-evidence proteins with a substantial amount of independent evidence (definition of substantial left open). Our software produces such a set and I imagine that other software does as well. The canonical proteins may be complementary to the possibly distinguished proteins. covering protein: one of a minimal set of independent-evidence proteins sufficient to explain all matched spectra. Such a set is needed to parsimoniously associate each peptide identification with one protein identification. 5. Possibly, add terms to describe proteins that are indistinguishable but where some peptide enzymatically favored in one protein over the other. This includes what Matt calls "terminal specificity", and also includes cases of K/Q ambiguity. sequence same-set protein, enzymatically-favored spectrum same-set protein, enzymatically-favored etc. Or, instead of introducing a gazillion new terms with the "enzymatically-favored" modifier, it could be specified elsewhere in the mzIdentML whether enzymatic favorability is considered. Our proposal allows the terminology to be more descriptive in ways that will allow the data consumer to better evaluate and use the data.

Neuroendocrine Protein 7B2 group representative; sequence sub-set (P05408) representative; independent-evidence, enzymatic favorability considered; canonical sequence same-set (P05408) representative; sequence same-set (enzymatically UNfavorable ) (P05408)

Heat Shock Protein group, part 1 of 2 (only representative proteins shown) independent-evidence; canonical independent-evidence; canonical independent-evidence; canonical OR marginally distinguished, depending on threshold sequence sub-set (enzymatically UNfavorable ) (P07900) sequence sub-set (enzymatically UNfavorable ) (P07900) Coloring problem <- This pep is misaligned; it belongs about 35 residues to the left

Heat Shock Protein group, part 2 of 2 independent-evidence; canonical independent-evidence; canonical independent-evidence; canonical OR marginally distinguished, depending on threshold sequence sub-set (enzymatically UNfavorable ) (P07900) sequence sub-set (enzymatically UNfavorable ) (P07900)

(only representative proteins shown) Complement C3 group (only representative proteins shown) Region of sequence identity and nearly 100% peptide coverage Region of non-identity; no peps observed Tiny region of non-identity; peps observed independent-evidence canonical covering P01024 Complement C3 sequence sub-set, enzymatically favored (P01024) independent-evidence, enzym. fav. considered marginally distinguished (P01024) covering IPI00739237 Distinguished by its fully-tryptic N-terminal peptide, which is semi-tryptic in P01024. independent-evidence marginally distinguished (P01024) covering IPI00887739 Distinguished by 4 peptides (3 with missed cleavages) encompassing this single residue difference. This is listed as a SNP in Swiss-Prot. C-terminal peptide is not observed, so this truncated form probably has not been seen. A8K2U0 Alpha-2-macroglobulin-like protein 1 Only one 7-residue peptide observed; this peptide is also seen in P01024 but the 2 proteins are unrelated sequence sub-set (P01024) ENSP00000406291 sequence sub-set (P01024) IPI00942927 sequence sub-set (P01024) These two sequences, which differ from each other in only 3 positions, appear to be potential splice variants of P01024, These probably have not been observed because the peptides spanning the splice junctions have not been observed. O95568 UPF0558 protein C1orf156 sequence sub-set (P01024) Only one 8-residue peptide observed; this peptide is also seen in P01024 but the two proteins are unrelated