Catalog of proteins encoded by human genome published

A special issue of the Journal of Proteome Research celebrates the 90% completion of the human proteome, a catalog of all the proteins encoded by the human genome. 

The international Human Proteome Organization (HUPO) released its draft human proteome Oct. 19, simultaneous with the journal's re-publication of the 60 most significant papers it has published in the last decade on the proteome. 

The journal editorial reviews the immensity and importance of HUPO's achievement and outlines its history. Its author, Christopher Overall, a biology professor at the University of British Columbia, is chair of the Chromosome-Centric Human Proteome Project. The editorial stresses the international aspect of the effort, with collaborating teams of scientists from around the world. It also notes that HUPO gives "free and open access to proteomic data."

Once published, all proteomic data are uploaded into databases in the ProteomeXchange Consortium, which are then annotated and made public.

Cataloguing the human proteome is especially important in helping mankind's understanding of human disease. The presence of certain proteins may protect against disease, while the absence or malformations of them may lead to greater risk of disease. As the editorial suggests, the proteome information may help researchers design drugs for treating specific diseases.

The editorial stresses that genomics cannot provide the information to decipher changes brought about in cells or tissue by microorganisms or viruses, but proteomics can. This is particularly relevant now in understanding COVID-19.

"Deciphering this new 'proteome code' is the challenge that lies ahead for the proteomics and HPP [Human Proteome Project] communities and for addressing the broken hyperbole springing from the euphoria of the publication of the human genome papers 20 years ago, when the media and pundits predicted the curing of some, if not all, human diseases within a few years," the editorial states.

The human proteome is more difficult characterize than the genome. As the editorial notes, the genome effort started in October 1990, and by April 2003 the accurate sequence of 99% of the human genome was announced. Advances in sequencing technology and computer power helped speed the effort. 

Currently about 10% of the proteome is "missing." These 1,899 "missing proteins," as they are known, are "spread across all 22 autosomes and the X and Y chromosomes."

Completing the proteome is inherently a more complex job. Instead of dealing only with the four nucleotides of DNA, the proteome basic elements are polypeptide chains of 20 amino acids. These undergo many modifications, which, the editorial notes, "together generate millions of proteoforms and a dynamic proteome." 

In addition, unlike DNA, which is found in almost all human cells, the missing proteins are not found in all cells, which would make them easier to find. 

To complete the task, the editorial notes, will take new, more sensitive technologies, better bioinformatics and better funding.

The editorial concludes: "For the next high-fidelity compendium of the full human proteome and to develop a broader understanding of life, human conscience, and disease, proteomics needs more data, more patients, more scientists – biochemists, geneticists, engineers, mathematicians, and bioinformaticians, and more doctors to understand life, individuality, personality, and disease. Science needs us all but now, more than ever, humanity needs more science."