neXtProt has announced in their February 2016 release that its metrics for assigning proteins as protein evidence 1 (PE1) as part of the Human Proteome Project now align with those proposed by PeptideAtlas in September 2015.
Our collaborators at neXtProt state:
Entries whose protein(s) existence is based on evidence at the transcript level (PE2), homology (PE3) or a prediction (gene model; PE4) were previously upgraded to evidence at the protein level (PE1) if the entry had (i) 2 proteotypic peptides 7 or 8 amino acids in length or (ii) 1 peptide at least 9 aa coming from mass spectrometry experiments in neXtProt. This rule has been made more stringent so as to be in sync with the PeptideAtlas/HPP criteria for validating proteins using mass spectrometry data (i.e., at least 2 proteotypic peptides 9 aa in length or more which differ in at least 1 amino acid and which are not overlapping) are now required for the protein evidence to be upgraded to PE1.
For more details click here.