Access Guide to Human Proteinpedia

Babylakshmi Muthusamy1, Joji Kurian Thomas2, T.S. Keshava Prasad2, Akhilesh Pandey3

1 Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India, 2 Amrita School of Biotechnology, Amrita University, Kollam, India, 3 McKusick‐Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology, and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.21
DOI:  10.1002/0471250953.bi0121s41
Online Posting Date:  March, 2013
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Human Proteinpedia ( is a publicly available proteome repository for sharing human protein data derived from multiple experimental platforms. It incorporates diverse features of the human proteome including protein‐protein interactions, enzyme‐substrate relationships, PTMs, subcellular localization, and expression of proteins in various human tissues and cell lines in diverse biological conditions including diseases. Through a publicly distributed annotation system developed especially for proteomic data, investigators across the globe can upload, view, and edit proteomic data even before they are published. Inclusion of information on investigators and laboratories that generated the data, as well as visualization of tandem mass spectra, stained tissue sections, protein/peptide microarrays, fluorescent micrographs, and western blots, ensures quality of proteomic data assimilated in Human Proteinpedia. Many of the protein annotations submitted to Human Proteinpedia have also been made available to the scientific community through Human Protein Reference Database (, another resource developed by our group. In this protocol, we describe how to submit, edit, and retrieve proteomic data in Human Proteinpedia. Curr. Protoc. Bioinform. 41:1.21.1‐1.21.15. © 2013 by John Wiley & Sons, Inc.

Keywords: mass spectrometry; tissue microarrays; biomarkers; disease proteomics; HPRD; proteotypic peptides; multiple reaction monitoring

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Table of Contents

  • Introduction
  • Basic Protocol 1: Querying Human Proteinpedia
  • Basic Protocol 2: Annotation of Protein Features Through Community Participation
  • Basic Protocol 3: Integration of Human Proteinpedia into HPRD
  • Basic Protocol 4: Data Download into Human Proteinpedia
  • Basic Protocol 5: Examination of Sample Annotation Files
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

   Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel‐Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25‐29.
   Garavelli, J.S. 2004. The RESID database of protein modifications as a resource and annotation tool. Proteomics 4:1527‐1533.
   Hamacher, M., Klose, J., Rossier, J., Marcus, K., and Meyer, H.E. 2004. Does understanding the brain need proteomics and does understanding proteomics need brains? Second HUPO HBPP Workshop hosted in Paris. Proteomics 4:1932‐1934.
   He, F. 2005. Human liver proteome project: Plan, progress, and perspectives. Mol. Cell. Proteom. 4:1841‐1848.
   Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y.L., Acharya, P.K., Ranganathan, P., Chaerkady, R., Keshava Prasad, T.S., and Pandey, A. 2009. Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Res. 37:D773‐D781.
   Kelso, J., Visagie, J., Theiler, G., Christoffels, A., Bardien, S., Smedley, D., Otgaar, D., Greyling, G., Jongeneel, C.V., McCarthy, M.I., Hide, T., and Hide, W. 2003. eVOC: A controlled vocabulary for unifying gene expression data. Genome Res. 13:1222‐1230.
   Kerrien, S., Orchard, S., Montecchi‐Palazzi, L., Aranda, B., Quinn, A.F., Vinod, N., Bader, G.D., Xenarios, I., Wojcik, J., Sherman, D., Tyers, M., Salama, J.J., Moore, S., Ceol, A., Chatr‐Aryamontri, A., Oesterheld, M., Stumpflen, V., Salwinski, L., Nerothin, J., Cerami, E., Cusick, M.E., Vidal, M., Gilson, M., Armstrong, J., Woollard, P., Hogue, C., Eisenberg, D., Cesareni, G., Apweiler, R., and Hermjakob, H. 2007. Broadening the horizon—level 2.5 of the HUPO‐PSI format for molecular interactions. BMC Biol. 5:44.
   Keshava Prasad, T.S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D.S., Sebastian, A., Rani, S., Ray, S., Harrys Kishore, C.J., Kanth, S., Ahmed, M., Kashyap, M.K., Mohmood, R., Ramachandra, Y.L., Krishna, V., Rahiman, B.A., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R., and Pandey, A. 2009. Human protein reference database‐2009 update. Nucleic Acids Res. 37:D767‐D772.
   Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W.H., Rompp, A., Neumann, S., Pizarro, A.D., Montecchi‐Palazzi, L., Tasman, N., Coleman, M., Reisinger, F., Souda, P., Hermjakob, H., Binz, P.A., and Deutsch, E.W. 2011. mzML‐a community standard for mass spectrometry data. Mol. Cell. Proteom. 10:R110.00133.
   Mathivanan, S., Ahmed, M., Ahn, N.G., Alexandre, H., Amanchy, R., Andrews, P.C., Bader, J.S., Balgley, B.M., Bantscheff, M., Bennett, K.L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S.K., Burlingame, A.S., Bustelo, X.R., Cagney, G., Cantin, G.T., Cardasis, H.L., Celis, J.E., Chaerkady, R., Chu, F., Cole, P.A., Costello, C.E., Cotter, R.J., Crockett, D., DeLany, J.P., De Marzo, A.M., DeSouza, L.V., Deutsch, E.W., Dransfield, E., Drewes, G., Droit, A., Dunn, M.J., Elenitoba‐Johnson, K., Ewing, R.M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J.M., Gnad, F., Goel, R., Gromov, P., Hanash, S.M., Hancock, W.S., Harsha, H.C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D.F., Hofmann, O., Horn, D.M., Hruban, R.H., Ibarrola, N., James, P., Jensen, O.N., Jensen, P.H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R.F., Korf, U., Korner, R., Kuster, B., Kwon, M.S., Lee, H.J., Lee, Y.J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M.S., Lobke, C., Loo, J.A., Mann, M., Martens, L., Martinez‐Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C.A., Mischak, H., Mohan, S.S., Mohmood, R., Molina, H., Moran, M.F., Morgan, J.D., Moritz, R., Morzel, M., Muddiman, D.C., Nalli, A., Navarro, J.D., Neubert, T.A., Ohara, O., Oliva, R., Omenn, G.S., Oyama, M., Paik, Y.K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E.F., Poirier, G.G., Prasad, T.S., Purvine, S.O., Rahiman, B.A., Ramachandran, P., Ramachandra, Y.L., Rice, R.H., Rick, J., Ronnholm, R.H., Salonen, J., Sanchez, J.C., Sayd, T., Seshi, B., Shankari, K., Sheng, S.J., Shetty, V., Shivakumar, K., Simpson, R.J., Sirdeshmukh, R., Siu, K.W., Smith, J.C., Smith, R.D., States, D.J., Sugano, S., Sullivan, M., Superti‐Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J.C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T.D., Vidal‐Taboada, J.M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J.R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P., and Pandey, A. 2008. Human Proteinpedia enables sharing of human protein data. Nat. Biotechnol. 26:164‐167.
   Medina‐Aunon, J.A., Carazo, J.M., and Albar, J.P. 2011. PRIDEViewer: A novel user‐friendly interface to visualize PRIDE XML files. Proteomics 11:334‐337.
   Omenn, G.S., Baker, M.S., and Aebersold, R. 2011. Recent workshops of the HUPO human plasma proteome project (HPPP): A bridge with the HUPO cardiovascular initiative and the emergence of SRM targeted proteomics. Proteomics 11:3439‐3443.
   Pruitt, K.D., Tatusova, T., Klimke, W., and Maglott, D.R. 2009. NCBI reference sequences: Current status, policy and new initiatives. Nucleic Acids Res. 37:D32‐D36.
   Smith, B.E., Hill, J.A., Gjukich, M.A., and Andrews, P.C. 2011. Tranche distributed repository and Methods Mol. Biol. 696:123‐145.
   Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S., Wernerus, H., Bjorling, L., and Ponten, F. 2010. Towards a knowledge‐based Human Protein Atlas. Nat. Biotechnol. 28:1248‐1250.
   UniProt, C. 2012. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40:D71‐D75.
Key References
   Mathivanan et al., 2008. See above
  This paper describes the multiple layers of contribution from the external laboratories and potential usefulness of integrating Human Proteinpedia into HPRD.
   Kandasamy et al., 2009. See above.
  Update of Mathivanan et al. () for the detailed explanation on various feature annotated in Human Proteinpedia and the potential uses of Human Proteinpedia data.
Internet Resources
  The Human Proteinpedia home page.
  The Human Proteinpedia download server.
  The Human Proteinpedia public distributed annotation server.
  The user's queries and data request are answered through this link.
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