The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.
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We would like to acknowledge the National Development and Research Institutes for some of the tissues. We acknowledge the assistance of V. Sandhya, V. Puttamallesh, U. Guha and B. Cole for help with analysis of some of the samples. We thank L. Lane and B. Amos for their assistance with the list of missing genes. This work was supported by an NIH roadmap grant for Technology Centers of Networks and Pathways (U54GM103520), NCI’s Clinical Proteomic Tumor Analysis Consortium initiative (U24CA160036), a contract (HHSN268201000032C) from the National Heart, Lung and Blood Institute and the Sol Goldman Pancreatic Cancer Research Center. The authors acknowledge the joint participation by the Adrienne Helis Malvin Medical Research Foundation and the Diana Helis Henry Medical Research Foundation through its direct engagement in the continuous active conduct of medical research in conjunction with The Johns Hopkins Hospital and the Johns Hopkins University School of Medicine and the Foundation’s Parkinson’s Disease Programs. The analysis work was partially supported by the National Resource for Network Biology (P41GM103504). A.Mah., S.K.Sh., P.S. and T.S.K.P. are supported by DBT Program Support on Neuroproteomics (BT/01/COE/08/05) to IOB and NIMHANS. H.G. is a Wellcome Trust-DBT India Alliance Early Career Fellow. We thank Council of Scientific and Industrial Research, University Grants Commission and Department of Science and Technology, Government of India for research fellowships for S.M.P., R.S.N., A.R., M.K., G.J.S., S.C., P.R., J.S., S.S.M., D.S.K., S.R., S.K.Sr., K.K.D., Y.S., A.S., S.D.Y., N.S., S.A. and G.D.
Extended data figures
This file contains a summary of results from proteogenomics analysis; a list of peptides indicating novel signal peptide cleavage sites; and a draft map of the human proteome.
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PPIExp: A Web-Based Platform for Integration and Visualization of Protein–Protein Interaction Data and Spatiotemporal Proteomics Data
Journal of Proteome Research (2019)