A cell-based approach to the human proteome project

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 10, 2012, Pages 1617-1624

  Kelleher, Neil L ^a,b  

^a NORTHWESTERN UNIVERSITY   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

Cell type; Human genome project; Human proteome project; Mass spectrometry; Protein isoforms; Top down proteomics

Indexed keywords

CELL TYPES; HUMAN GENOME PROJECT; HUMAN PROTEOME; PROTEIN ISOFORMS; PROTEOMICS;

CELLS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PROTEINS;

CYTOLOGY;

HISTONE; PROTEOME;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CELL SPECIFICITY; CELLULAR DISTRIBUTION; COST EFFECTIVENESS ANALYSIS; DNA DETERMINATION; FLUORESCENCE ACTIVATED CELL SORTING; GENE DOSAGE; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN GENOME PROJECT; HUMAN PROTEOME PROJECT; MASS SPECTROMETRY; NOMENCLATURE; PERFORMANCE MEASUREMENT SYSTEM; PLEIOTROPY; PROCESS DEVELOPMENT; PROCESS TECHNOLOGY; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; PROTEOMICS; STRUCTURE ANALYSIS;

CELLS; HUMANS; MASS SPECTROMETRY; PROTEIN ISOFORMS; PROTEINS; PROTEOME; PROTEOMICS;

EID: 84868229162     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0469-9     Document Type: Article

References (22)

1. Kaiser, J.: Proteomics. Public-private group maps out initiatives. Science 296, 827 (2002)
2. Cottingham, K.: HUPO's Human Proteome Project: the next big thing? J. Proteome Res. 7(6), 2192 (2008)
3. Legrain, P., Aebersold, R., Archakov, A., Bairoch, A., Bala, K., Beretta, L., Bergeron, J., Borchers, C.H., Corthals, G.L., Costello, C.E., Deutsch, E.W., Domon, B., Hancock, W., He, F., Hochstrasser, D., Marko-Varga, G., Salekdeh, G.H., Sechi, S., Snyder, M., Srivastava, S., Uhlén, M., Wu, C.H., Yamamoto, T., Paik, Y.K., Omenn, G.S.: The human proteome project: current state and future direction. Mol. Cell Proteom. 10, (2011). doi:10.1074/mcp. M111.009993
4. Rabilloud, T., Hochstrasser, D., Simpson, R.J.: Is a gene-centric human proteome project the best way for proteomics to serve biology? Proteomics 10, 3067-3072 (2010)
5. Paik, Y.K., Jeong, S.K., Omenn, G.S., Uhlen, M., Hanash, S., Cho, S.Y., Lee, H.J., Na, K., Choi, E.Y., Yan, F., Zhang, F., Zhang, Y., Snyder, M., Cheng, Y., Chen, R., Marko-Varga, G., Deutsch, E.W., Kim, H., Kwon, J.Y., Aebersold, R., Bairoch, A., Taylor, A.D., Kim, K.Y., Lee, E.Y., Hochstrasser, D., Legrain, P., Hancock, W.S.: The chromosome-centric Human Proteome Project for cataloging proteins encoded in the genome. Nat. Biotechnol. 30, 221-223 (2012)
6. Paik, Y.K., Omenn, G.S., Uhlen, M., Hanash, S., Marko-Varga, G., Aebersold, R., Bairoch, A., Yamamoto, T., Legrain, P., Lee, H.J., Na, K., Jeong, S.K., He, F., Binz, P.A., Nishimura, T., Keown, P., Baker, M.S., Yoo, J.S., Garin, J., Archakov, A., Bergeron, J., Salekdeh, G.H., Hancock, W.S.: Standard guidelines for the chromosome-centric human proteome project. J. Proteome Res. 11, 2005-2013 (2012)
7. Montecchi-Palazzi, L., Beavis, R., Binz, P.A., Chalkley, R.J., Cottrell, J., Creasy, D., Shofstahl, J., Seymour, S.L., Garavelli, J.S.: The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol. 26, 864-866 (2008)
8. Addona, T.A., Abbatiello, S.E., Schilling, B., Skates, S.J., Mani, D.R., Bunk, D.M., Spiegelman, C.H., Zimmerman, L.J., Ham, A.J., Keshishian, H., Hall, S.C., Allen, S., Blackman, R.K., Borchers, C.H., Buck, C., Cardasis, H.L., Cusack, M.P., Dodder, N.G., Gibson, B.W., Held, J.M., Hiltke, T., Jackson, A., Johansen, E.B., Kinsinger, C.R., Li, J., Mesri, M., Neubert, T.A., Niles, R.K., Pulsipher, T.C., Ransohoff, D., Rodriguez, H., Rudnick, P.A., Smith, D., Tabb, D.L., Tegeler, T.J., Variyath, A.M., Vega-Montoto, L.J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J.R., Zhao, L., Anderson, N.L., Fisher, S.J., Liebler, D.C., Paulovich, A.G., Regnier, F.E., Tempst, P., Carr, S.A.: Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641 (2009)
9. Di Palma, S., Stange, D., van de Wetering, M., Clevers, H., Heck, A.J., Mohammed, S.: Highly sensitive proteome analysis of FACS-sorted adult colon stem cells. J. Proteome Res. 10, 3814-3819 (2011)
10. Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R., Bibel, M., Schiess, R., Aebersold, R., Watts, J.D.: Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol. 27, 378-386 (2009)
11. Bendall, S.C., Simonds, E.F., Qiu, P., Amir, E.-A.D., Krutzik, P.O., Finck, R., Bruggner, R.V., Melamed, R., Trejo, A., Ornatsky, O.I., Balderas, R.S., Plevritis, S.K., Sachs, K., Pe'er, D., Tanner, S.D., Nolan, G.P.: Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332, 687-696 (2011)
12. The curators of Cellpedia have extended the 230 classically assigned cell types by considering factors like tissue context to create an hierarchical system with 2718 differentiated and 66 stem cell types now classified into distinct taxonomic keys in version 1.7. Available at: http://cellpedia.cbrc.jp/. Accessed March 26, 2012
13. Misek, D.E., Kuick, R., Wang, H., Galchev, V., Deng, B., Zhao, R., Tra, J., Pisano, M.R., Amunugama, R., Allen, D., Walker, A.K., Strahler, J.R., Andrews, P., Omenn, G.S., Hanash, S.M.: A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics 5, 3343-3352 (2005)
14. Tran, J.C., Zamdborg, L., Ahlf, D.R., Lee, J.E., Catherman, A.D., Durbin, K.R., Tipton, J.D., Vellaichamy, A., Kellie, J.F., Li, M., Wu, C., Sweet, S.M., Early, B.P., Siuti, N., LeDuc, R.D., Compton, P.D., Thomas, P.M., Kelleher, N.L.: Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480, 254-258 (2011)
15. Nagaraj, N., Wisniewski, J.R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., Mann, M.: Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, (2011). doi:10.1038/msb.2011.81
16. Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., Aebersold, R.: The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, (2011). doi:10.1038/msb.2011. 82
17. Zhou, M., Morgner, N., Barrera, N.P., Politis, A., Isaacson, S.C., Matak-Vinković, D., Murata, T., Bernal, R.A., Stock, D., Robinson, C.V.: Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding. Science 334, 380-385 (2011)
18. Yates, J.R.I.I.I., Gilchrist, A., Howell, K.E., Bergeron, J.J.: Proteomics of organelles and large cellular structures. Nat. Rev. Mol. Cell Biol. 6, 702-714 (2005)
19. Gatto, L., Vizcaino, J.A., Hermjakob, H., Huber, W., Lilley, K.S.: Organelle proteomics experimental designs and analysis. Proteomics 10, 3957 (2010)
20. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010)
21. Economic Impact of the Human Genome Project. Battelle Memorial Institute. Available at: http://www.unitedformedicalresearch.com/wp-content/uploads/2012/ 08/Economic-Impact-of-the-Human-Genome-Project.pdf. Accessed May 2011
22. Prabakaran, S., Lippens, G., Steen, H., Gunawardena, J., Posttranslational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. WIREs Syst. Biol. Med. (2012). doi:10.1002/wsbm.1185