Highlights of the Biology and Disease-driven Human Proteome Project, 2015–2016

Abstract

The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of “popular protein sets” for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.

Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV

“…Now there are 22 B/D-HPP teams, including eight formed since 2013 (Van Eyk et al). 31 Cross-B/D initiatives include the development of SRM strategies, reagents, spectral libraries, and assays 20 and the popular protein sets for targeted proteomics studies based on bibliometric studies of Lam et al 32 for the cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal organ systems. When the C-HPP was officially launched in 2012, 2,3 the first phase of identifying proteins and proteoforms was projected to require 6 years, followed by a second phase of extensive biological studies for 4 years.…”

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

“…There are research groups dedicatedly working in the fields of both discovery and targeted proteomics. Several proof‐of‐principle studies are being carried out worldwide, demonstrating the ability of proteomics to replace old techniques as well as improvements in sample preparation, instrumentation, and data analysis algorithms . In fact, a huge amount of data on these aspects is publicly available .…”

“…A recent review discussed using the targeted proteomics approach for the measurement of circulating insulin growth factor‐1 (IGF1) for routine performance in clinical settings . Similarly, the development of MRM assays in the field of cancer clinical management, pathogen diagnosis, and widespread chronic diseases such as diabetes would help to bring targeted proteomics in practice in the near future …”

Advances of the HUPO Human Proteome Project with broad applications for life sciences research

“…This approach to cardiovascular diseases was demonstrated by Jennifer van Eyk in her keynote address in Taipei. There are now 22 Biology and Disease teams who are advised to apply this approach [5]. …”