A draft map of the human proteome

Min Sik Kim; Sneha M. Pinto; Derese Getnet; Raja Sekhar Nirujogi; Srikanth S. Manda; Raghothama Chaerkady; Anil K. Madugundu; Dhanashree S. Kelkar; Ruth Isserlin; Shobhit Jain; Joji K. Thomas; Babylakshmi Muthusamy; Pamela Leal-Rojas; Praveen Kumar; Nandini A. Sahasrabuddhe; Lavanya Balakrishnan; Jayshree Advani; Bijesh George; Santosh Renuse; Lakshmi Dhevi N. Selvan; Arun H. Patil; Vishalakshi Nanjappa; Aneesha Radhakrishnan; Samarjeet Prasad; 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; Keshav Mudgal; Aditi Chatterjee; Tai Chung Huang; Jun Zhong; Xinyan Wu; Patrick G. Shaw; Donald Freed; Muhammad S. Zahari; Kanchan K. Mukherjee; Subramanian Shankar; Anita Mahadevan; Henry Lam; Christopher J. Mitchell; Susarla Krishna Shankar; Parthasarathy Satishchandra; John T. Schroeder; Ravi Sirdeshmukh; Anirban Maitra; Steven D. Leach; Charles G. Drake; Marc K. Halushka; T. S.Keshava Prasad; Ralph H. Hruban; Candace L. Kerr; Gary D. Bader; Christine A. Iacobuzio-Donahue; Harsha Gowda; Akhilesh Pandey

doi:10.1038/nature13302

A draft map of the human proteome

Min Sik Kim
, Sneha M. Pinto
, Derese Getnet
, Raja Sekhar Nirujogi
, Srikanth S. Manda
, Raghothama Chaerkady
, Anil K. Madugundu
, Dhanashree S. Kelkar
, Ruth Isserlin
, Shobhit Jain
, Joji K. Thomas
, Babylakshmi Muthusamy
, Pamela Leal-Rojas
, Praveen Kumar
, Nandini A. Sahasrabuddhe
, Lavanya Balakrishnan
, Jayshree Advani
, Bijesh George
, Santosh Renuse
, Lakshmi Dhevi N. Selvan

Arun H. Patil, Vishalakshi Nanjappa, Aneesha Radhakrishnan, Samarjeet Prasad, 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, Keshav Mudgal, Aditi Chatterjee, Tai Chung Huang, Jun Zhong, Xinyan Wu, Patrick G. Shaw, Donald Freed, Muhammad S. Zahari, Kanchan K. Mukherjee, Subramanian Shankar, Anita Mahadevan, Henry Lam, Christopher J. Mitchell, Susarla Krishna Shankar, Parthasarathy Satishchandra, John T. Schroeder, Ravi Sirdeshmukh, Anirban Maitra, Steven D. Leach, Charles G. Drake, Marc K. Halushka, T. S.Keshava Prasad, Ralph H. Hruban, Candace L. Kerr, Gary D. Bader, Christine A. Iacobuzio-Donahue, Harsha Gowda, Akhilesh Pandey

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Research output: Contribution to journal › Article › peer-review

1831 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	575-581
Number of pages	7
Journal	Nature
Volume	509
Issue number	7502
DOIs	https://doi.org/10.1038/nature13302
Publication status	Published - 29 May 2014

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Protein–protein interaction networks
Protein sequencing
Proteomic analysis

ASJC Scopus subject areas

General

Access to Document

10.1038/nature13302

Cite this

Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., Thomas, J. K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N. A., Balakrishnan, L., Advani, J., George, B., Renuse, S., ... Pandey, A. (2014). A draft map of the human proteome. Nature, 509(7502), 575-581. https://doi.org/10.1038/nature13302

@article{8c55b2a6ccbe4684b064d7e9791ec338,

title = "A draft map of the human proteome",

abstract = "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.",

keywords = "Protein–protein interaction networks, Protein sequencing, Proteomic analysis",

author = "Kim, \{Min Sik\} and Pinto, \{Sneha M.\} and Derese Getnet and Nirujogi, \{Raja Sekhar\} and Manda, \{Srikanth S.\} and Raghothama Chaerkady and Madugundu, \{Anil K.\} and Kelkar, \{Dhanashree S.\} and Ruth Isserlin and Shobhit Jain and Thomas, \{Joji K.\} and Babylakshmi Muthusamy and Pamela Leal-Rojas and Praveen Kumar and Sahasrabuddhe, \{Nandini A.\} and Lavanya Balakrishnan and Jayshree Advani and Bijesh George and Santosh Renuse and Selvan, \{Lakshmi Dhevi N.\} and Patil, \{Arun H.\} and Vishalakshi Nanjappa and Aneesha Radhakrishnan and Samarjeet Prasad and Tejaswini Subbannayya and Rajesh Raju and Manish Kumar and Sreenivasamurthy, \{Sreelakshmi K.\} and Arivusudar Marimuthu and Sathe, \{Gajanan J.\} and Sandip Chavan and Datta, \{Keshava K.\} and Yashwanth Subbannayya and Apeksha Sahu and Yelamanchi, \{Soujanya D.\} and Savita Jayaram and Pavithra Rajagopalan and Jyoti Sharma and Murthy, \{Krishna R.\} and Nazia Syed and Renu Goel and Khan, \{Aafaque A.\} and Sartaj Ahmad and Gourav Dey and Keshav Mudgal and Aditi Chatterjee and Huang, \{Tai Chung\} and Jun Zhong and Xinyan Wu and Shaw, \{Patrick G.\} and Donald Freed and Zahari, \{Muhammad S.\} and Mukherjee, \{Kanchan K.\} and Subramanian Shankar and Anita Mahadevan and Henry Lam and Mitchell, \{Christopher J.\} and Shankar, \{Susarla Krishna\} and Parthasarathy Satishchandra and Schroeder, \{John T.\} and Ravi Sirdeshmukh and Anirban Maitra and Leach, \{Steven D.\} and Drake, \{Charles G.\} and Halushka, \{Marc K.\} and Prasad, \{T. S.Keshava\} and Hruban, \{Ralph H.\} and Kerr, \{Candace L.\} and Bader, \{Gary D.\} and Iacobuzio-Donahue, \{Christine A.\} and Harsha Gowda and Akhilesh Pandey",

note = "Funding Information: 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. Funding Information: Acknowledgements 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{\textquoteright}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 ResearchCenter. The authorsacknowledge the jointparticipationbythe AdrienneHelis 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{\textquoteright}s Parkinson{\textquoteright}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. Copyright: Copyright 2014 Elsevier B.V., All rights reserved.",

year = "2014",

month = may,

day = "29",

doi = "10.1038/nature13302",

language = "English",

volume = "509",

pages = "575--581",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7502",

}

Kim, MS, Pinto, SM, Getnet, D, Nirujogi, RS, Manda, SS, Chaerkady, R, Madugundu, AK, Kelkar, DS, Isserlin, R, Jain, S, Thomas, JK, Muthusamy, B, Leal-Rojas, P, Kumar, P, Sahasrabuddhe, NA, Balakrishnan, L, Advani, J, George, B, Renuse, S, Selvan, LDN, Patil, AH, Nanjappa, V, Radhakrishnan, A, Prasad, S, Subbannayya, T, Raju, R, Kumar, M, Sreenivasamurthy, SK, Marimuthu, A, Sathe, GJ, Chavan, S, Datta, KK, Subbannayya, Y, Sahu, A, Yelamanchi, SD, Jayaram, S, Rajagopalan, P, Sharma, J, Murthy, KR, Syed, N, Goel, R, Khan, AA, Ahmad, S, Dey, G, Mudgal, K, Chatterjee, A, Huang, TC, Zhong, J, Wu, X, Shaw, PG, Freed, D, Zahari, MS, Mukherjee, KK, Shankar, S, Mahadevan, A, Lam, H, Mitchell, CJ, Shankar, SK, Satishchandra, P, Schroeder, JT, Sirdeshmukh, R, Maitra, A, Leach, SD, Drake, CG, Halushka, MK, Prasad, TSK, Hruban, RH, Kerr, CL, Bader, GD, Iacobuzio-Donahue, CA, Gowda, H & Pandey, A 2014, 'A draft map of the human proteome', Nature, vol. 509, no. 7502, pp. 575-581. https://doi.org/10.1038/nature13302

TY - JOUR

T1 - A draft map of the human proteome

AU - Kim, Min Sik

AU - Pinto, Sneha M.

AU - Getnet, Derese

AU - Nirujogi, Raja Sekhar

AU - Manda, Srikanth S.

AU - Chaerkady, Raghothama

AU - Madugundu, Anil K.

AU - Kelkar, Dhanashree S.

AU - Isserlin, Ruth

AU - Jain, Shobhit

AU - Thomas, Joji K.

AU - Muthusamy, Babylakshmi

AU - Leal-Rojas, Pamela

AU - Kumar, Praveen

AU - Sahasrabuddhe, Nandini A.

AU - Balakrishnan, Lavanya

AU - Advani, Jayshree

AU - George, Bijesh

AU - Renuse, Santosh

AU - Selvan, Lakshmi Dhevi N.

AU - Patil, Arun H.

AU - Nanjappa, Vishalakshi

AU - Radhakrishnan, Aneesha

AU - Prasad, Samarjeet

AU - Subbannayya, Tejaswini

AU - Raju, Rajesh

AU - Kumar, Manish

AU - Sreenivasamurthy, Sreelakshmi K.

AU - Marimuthu, Arivusudar

AU - Sathe, Gajanan J.

AU - Chavan, Sandip

AU - Datta, Keshava K.

AU - Subbannayya, Yashwanth

AU - Sahu, Apeksha

AU - Yelamanchi, Soujanya D.

AU - Jayaram, Savita

AU - Rajagopalan, Pavithra

AU - Sharma, Jyoti

AU - Murthy, Krishna R.

AU - Syed, Nazia

AU - Goel, Renu

AU - Khan, Aafaque A.

AU - Ahmad, Sartaj

AU - Dey, Gourav

AU - Mudgal, Keshav

AU - Chatterjee, Aditi

AU - Huang, Tai Chung

AU - Zhong, Jun

AU - Wu, Xinyan

AU - Shaw, Patrick G.

AU - Freed, Donald

AU - Zahari, Muhammad S.

AU - Mukherjee, Kanchan K.

AU - Shankar, Subramanian

AU - Mahadevan, Anita

AU - Lam, Henry

AU - Mitchell, Christopher J.

AU - Shankar, Susarla Krishna

AU - Satishchandra, Parthasarathy

AU - Schroeder, John T.

AU - Sirdeshmukh, Ravi

AU - Maitra, Anirban

AU - Leach, Steven D.

AU - Drake, Charles G.

AU - Halushka, Marc K.

AU - Prasad, T. S.Keshava

AU - Hruban, Ralph H.

AU - Kerr, Candace L.

AU - Bader, Gary D.

AU - Iacobuzio-Donahue, Christine A.

AU - Gowda, Harsha

AU - Pandey, Akhilesh

N1 - Funding Information: 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. Funding Information: Acknowledgements 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 ResearchCenter. The authorsacknowledge the jointparticipationbythe AdrienneHelis 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. Copyright: Copyright 2014 Elsevier B.V., All rights reserved.

PY - 2014/5/29

Y1 - 2014/5/29

N2 - 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.

AB - 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.

KW - Protein–protein interaction networks

KW - Protein sequencing

KW - Proteomic analysis

UR - https://www.scopus.com/pages/publications/84901599553

U2 - 10.1038/nature13302

DO - 10.1038/nature13302

M3 - Article

C2 - 24870542

AN - SCOPUS:84901599553

SN - 0028-0836

VL - 509

SP - 575

EP - 581

JO - Nature

JF - Nature

IS - 7502

ER -

A draft map of the human proteome

Abstract

UN SDGs

Keywords

ASJC Scopus subject areas

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