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A draft map of the human proteome

Nature volume 509, pages 575581 (29 May 2014) | Download Citation


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 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.

Author information

Author notes

    • Candace L. Kerr

    Present address: Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.


  1. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

    • Min-Sik Kim
    • , Derese Getnet
    • , Raghothama Chaerkady
    • , Pamela Leal-Rojas
    • , Samarjeet Prasad
    • , Tai-Chung Huang
    • , Jun Zhong
    • , Xinyan Wu
    • , Patrick G. Shaw
    • , Donald Freed
    • , Christopher J. Mitchell
    • , Steven D. Leach
    •  & Akhilesh Pandey
  2. Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

    • Min-Sik Kim
    • , Raghothama Chaerkady
    • , Xinyan Wu
    • , Muhammad S. Zahari
    •  & Akhilesh Pandey
  3. Institute of Bioinformatics, International Tech Park, Bangalore 560066, India

    • Sneha M. Pinto
    • , Raja Sekhar Nirujogi
    • , Srikanth S. Manda
    • , Anil K. Madugundu
    • , Dhanashree S. Kelkar
    • , Joji K. Thomas
    • , Babylakshmi Muthusamy
    • , Praveen Kumar
    • , Nandini A. Sahasrabuddhe
    • , Lavanya Balakrishnan
    • , Jayshree Advani
    • , Bijesh George
    • , Santosh Renuse
    • , Lakshmi Dhevi N. Selvan
    • , Arun H. Patil
    • , Vishalakshi Nanjappa
    • , Aneesha Radhakrishnan
    • , Tejaswini Subbannayya
    • , Rajesh Raju
    • , Manish Kumar
    • , Sreelakshmi K. Sreenivasamurthy
    • , Arivusudar Marimuthu
    • , Gajanan J. Sathe
    • , Sandip Chavan
    • , Keshava K. Datta
    • , Yashwanth Subbannayya
    • , Apeksha Sahu
    • , Soujanya D. Yelamanchi
    • , Savita Jayaram
    • , Pavithra Rajagopalan
    • , Jyoti Sharma
    • , Krishna R. Murthy
    • , Nazia Syed
    • , Renu Goel
    • , Aafaque A. Khan
    • , Sartaj Ahmad
    • , Gourav Dey
    • , Aditi Chatterjee
    • , Ravi Sirdeshmukh
    • , T. S. Keshava Prasad
    • , Harsha Gowda
    •  & Akhilesh Pandey
  4. Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA

    • Derese Getnet
    •  & Akhilesh Pandey
  5. The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada

    • Ruth Isserlin
    • , Shobhit Jain
    •  & Gary D. Bader
  6. Department of Pathology, Universidad de La Frontera, Center of Genetic and Immunological Studies-Scientific and Technological Bioresource Nucleus, Temuco 4811230, Chile

    • Pamela Leal-Rojas
  7. School of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK

    • Keshav Mudgal
  8. Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India

    • Kanchan K. Mukherjee
  9. Department of Internal Medicine Armed Forces Medical College, Pune 411040, India

    • Subramanian Shankar
  10. Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India

    • Anita Mahadevan
    •  & Susarla Krishna Shankar
  11. Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India

    • Anita Mahadevan
    •  & Susarla Krishna Shankar
  12. Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong

    • Henry Lam
  13. Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India

    • Parthasarathy Satishchandra
  14. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA

    • John T. Schroeder
  15. The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA

    • Anirban Maitra
    • , Marc K. Halushka
    • , Ralph H. Hruban
    • , Christine A. Iacobuzio-Donahue
    •  & Akhilesh Pandey
  16. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA

    • Anirban Maitra
    • , Charles G. Drake
    • , Ralph H. Hruban
    • , Christine A. Iacobuzio-Donahue
    •  & Akhilesh Pandey
  17. Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA

    • Steven D. Leach
    •  & Christine A. Iacobuzio-Donahue
  18. Departments of Immunology and Urology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA

    • Charles G. Drake
  19. Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine Baltimore, Maryland 21205, USA

    • Candace L. Kerr
  20. Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana 70130, USA

    • Akhilesh Pandey


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A.P., H.G., R.C., M.-S.K. designed the study; A.P., H.G., M.-S.K. managed the study; D.G., C.L.K., C.A.I.-D., K.R.M. collected human cells/tissues; M.-S.K., R.C., D.G. developed the pipeline of experiment and analysis; D.G., M.-S.K., S.M.P., K.M., R.C., S.R., J.Z., X.W., P.G.S., M.S.Z., T.-C.H. prepared peptide samples for LC-MS/MS; M.-S.K., R.S.N., S.M.P., R.C., D.S.K., S.R., G.J.S. performed LC-MS/MS; M.-S.K., S.M.P., S.P., S.S.M., C.J.M., J.A. and A.K.M. processed MS data and managed data; A.K.M., S.S.M., B.G., A.H.P., Y.S., M.-S.K. performed comparison analysis with PeptideAtlas, neXtProt and GPMDB; R.I., S.Jai., G.D.B. performed interaction and complex analysis; M.-S.K., S.M.P., S.S.M., P.K., A.K.M., N.A.S., R.S.N., L.B., L.D.N.S., D.S.K., V.N., A.R., T.S., M.K., S.K.Sr., G.D., A.Mar., R.R., S.C., K.K.D., A.S., S.D.Y., S.Jay., P.R., A.H.P., B.G., J.S., N.S., R.G., G.J.S., A.A.K., S.A., D.F., T.S.K.P., H.G., A.P. performed proteogenomic analysis; A.C., H.L., R.S., J.T.S., K.K.M., S.S., A.Mah., S.K.Sh., P.S., S.D.L., C.G.D., A.Mai., M.K.H., R.H.H., C.L.K., C.A.I.-D. assisted with analysis of the data; M.-S.K., S.M.P., T.-C.H., P.L.-R. performed western blot experiments; M.-S.K., J.K.T., A.K.M., B.M., S.P., S.M.P. designed the Human Proteome Map web portal; M.-S.K., A.K.M., J.K.T. generated selected reaction monitoring (SRM) database; M.-S.K., K.M., G.D., S.M.P., S.S.M. illustrated figures with help of other authors; A.P., M.-S.K., H.G. wrote the manuscript with inputs from other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Harsha Gowda or Akhilesh Pandey.

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium ( via the PRIDE partner repository with the dataset identifier PXD000561.

Extended data

Supplementary information

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    Supplementary Information

    This file contains a Supplementary Discussion and additional references.

  2. 2.

    Supplementary Data

    This file contains Supplementary Data.

Excel files

  1. 1.

    Supplementary Table 1

    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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