The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list, the draft human proteome, confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on the sequence variants, post-translational modifications, and splice isoforms of those proteins, and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major mass spectrometry datasets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.0 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [www.thehpp.org/guidelines]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012, but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false-positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely-mapping (proteotypic) peptides of at least 9 aa in length. There are 2949 missing proteins (PE2+3+4) as the baseline for submissions for the 4th annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMdb has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about PTMs, SAAVs, and splice isoforms. Meanwhile, the Biology and Disease-driven B/D-HPP has created comprehensive SRM resources, generated popular-protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.