The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Abstract

The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

Identification of Potential Therapeutic Targets on the Level of DNA/mRNAs, Proteins and Metabolites: A Systematic Mapping Review of Scientific Texts’ Fragments from Open Targets

“…Our results suggest that given the number of genomic and transcriptomic evidence of the role of distinct biological macromolecules in pathology, there is a clear need to translate them into evidence on the level of proteins and metabolites [ 2 , 8 ]. Furthermore, since genes and their transcripts rarely act in the cell by themselves, more direct evidence may be of greater value for the basic and applied studies.…”

“…Instead, our results indicate the prevalence of genomic and transcriptomic evidence for the role of distinct biological macromolecules in pathology. Since genes and their transcripts rarely act in the cell by themselves and more direct evidence may be of greater value for the basic and applied studies of potential therapeutic targets, there is a clear need to translate the DNA/RNAs evidence into the ones on the level of proteins and metabolites [ 2 , 8 ].…”

Transcriptomics and Spatial Proteomics for Discovery and Validation of Missing Proteins in the Human Ovary

“…The Human Proteome Project (HPP) is an international initiative led by the Human Proteome Organization (HUPO), with the primary goal of comprehensively characterizing and understanding the human proteome . Accordingly, the neXtProt knowledge database (www.nextprot.org) updates its Protein Existence (PE) classification every year .…”

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

“…The Human Proteome Project (HPP) 14 launched by Human Proteome Organization (HUPO) has reported the community-based ten-year achievement of a high-stringency proteome blueprint of 17,874 Protein Evidence 1 (PE1) proteins in 2020, covering 90.4% of the human proteome 15 . A pan-human spectral library (PHL), containing 149,130 peptide precursors and 10,322 proteins, was developed to analyze Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) data acquired on SCIEX TripleTOF Systems 8 .…”