. 2021 Aug 19;33(11):3421–3453. doi: 10.1093/plcell/koab211

Table 2.

Protein identification confidence tiers and categories in the Arabidopsis PeptideAtlas build

Category^a	Definition
Tier 1: Canonical	Protein has at least two uniquely mapping non-nested peptides of at least 9 residues with at least 18 residues of total coverage.
Tier 2: Indistinguishable representative	Protein is selected as the representative of a set of proteins that are different in sequence but cannot be disambiguated based on the detected peptides. All peptides are shared with all group members. Others are “Indistinguishable”.
Tier 3: Representative	Protein is selected a representative in a situation more complex than a set of indistinguishable, where several proteins have shared peptides and at least some of the proteins must have been detected but it is not possible to determine which ones.
Tier 4: Marginally distinguished	Protein that shares several peptides with a canonical protein, but also has one uniquely mapping peptide that appears to distinguish it from the canonical.
Tier 5: Weak	Protein has at least one uniquely mapping peptide of 9 residues in length but does not meet the criteria for canonical.
Tier 6: Insufficient evidence	Protein has one or more uniquely mapping peptides but none reach 9 residues in length.
Tier 7: Indistinguishable	Protein is part of a set of proteins that cannot be disambiguated and it not selected as a leader of the group.
Tier 8: Subsumed	Protein has only shared peptides and is not needed to explain the peptide evidence.
Tier 9: Identical	Protein has an identical protein sequence to another one, and this one is effectively removed from category competition. Its partner may be canonical.
Tier 10: Not observed	Protein has no peptides above our PSM significance threshold. It may have low significant PSMs, but these are not considered.

Category^b	Definition

Canonical (as in tier 1 in Table 2^a)	Protein has at least two uniquely mapping non-nested peptides of at least 9 residues with at least 18 residues of total coverage
Uncertain (tiers 2–7 in Table 2^a)	Protein has too few uniquely mapping peptides of ≥ 9 aa to qualify for canonical status and may also have one or more shared peptides with other proteins.
Redundant (tiers 8 and 9 in Table 2^a)	Protein has only peptides that are can be assigned to other entries and thus these proteins are not needed to explain the observed peptide evidence.
Not Observed (tier 10 in Table 2^a)	Protein has no peptides above our PSM significance threshold. It may have low significance PSMs, but these are not considered.

^{^a}

Panel A: List of protein identification confidence tiers in the Arabidopsis PeptideAtlas build. Note that for each gene locus, only one gene model was counted using model .1 as default, unless there were specific matched peptides that could specifically distinguish more than one model, thereby receiving classification as tier 1 or 2.

^{^b}

Panel B: List of protein identification confidence tiers in the Arabidopsis PeptideAtlas build. Note that for each gene locus, only one gene model was counted using model .1 as default, unless there were specific matched peptides that could specifically distinguish more than one model, thereby receiving classification as canonical or uncertain.