Table 1.

Numbers of Proteins Classified in neXtProt Protein Existence Evidence Levels PE1,2,3,4 from 2012 to 2020, Showing Remarkable Progress in Confidently Identifying Predicted Human Proteins as PE1^a

PE level/neXtProt release	2012–02	2013–09	2014–10	2016–01	2017–01	2018–01	2019–01	2020–01
l: Evidence at Protein level	13 975	15 646	16 491	16 518	17 008	17 470	17 694	17 874
2: Evidence at transcript level	5205	3570	2647	2290	1939	1660	1548	1596
3: Inferred from homology	218	187	214	565	563	452	510	253
4: Predicted	88	87	87	94	77	74	71	50
MP = PE2 + PE3 + PE4	5511	3844	2948	2949	2579	2186	2129	1899
Human PeptideAtlas canonical proteins	12 509	13 377	14 928	14 569	15 173	15 798	16 293	16 655

^aAs of 2020–01, PE1/PE1 + 2 + 3 + 4 = 17 874/19 773 = 90.4% now PE1. The PE2,3,4 proteins are still “missing proteins” (MP). Dates represent the neXtProt releases used as baseline for the annual HPP metrics papers.^2–9 More stringent Guidelines 2.1 were imposed in time for the 2016–01 release.¹¹ Since 2016, the January release of neXtProt has served as the annual baseline. The final row shows the critical contribution of canonical proteins resulting from PeptideAtlas reanalyses of available MS datasets (see text and Figure 1).