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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Proteomics

  • To screen for proteins possibly responsible for 5-FU resistance, cells resistant to 5-FU were derived from human colon cancer cell lines and two-dimensional gel electrophoresis-based comparative proteomics was done [1].
  • Significantly, the reduction in mitochondrial complex V levels in the P301L tau mice revealed using proteomics was also confirmed as decreased in human P301L FTDP-17 (frontotemporal dementia with parkinsonism linked to chromosome 17) brains [2].
  • Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication [3].
  • Analysis of the quorum-sensing regulon of the opportunistic pathogen Burkholderia cepacia H111 by proteomics [4].
  • Breast cancer proteomics has already identified proteins of potential clinical interest, such as the molecular chaperone 14-3-3 sigma and the heat shock protein HSP90, and technological innovations such as large scale and high throughput analysis are now driving the field [5].

Psychiatry related information on Proteomics

  • We used proteomics to detect differences in protein expression between control, DS and Alzheimer's disease brains: In five individual brain regions of 9 individuals of each group we performed two dimensional electrophoresis with MALDI--identification of proteins and determined mRNA levels of DRP-2 [6].

High impact information on Proteomics

  • Comparative genomics and proteomics data implicate MKS1 in ciliary functions [7].
  • Using a proteomics approach, we have identified a complex comprised of Shoc2/Sur-8 and the catalytic subunit of protein phosphatase 1 (PP1c) as a highly specific M-Ras effector [8].
  • Here we combine functional proteomics with selective activation and inhibition of MKK1/2, in order to identify cellular targets regulated by the MKK/ERK cascade [9].
  • Using a targeted proteomics approach, we screened renal protein extracts with rabbit polyclonal antibodies directed to each of the major Na transporters expressed along the nephron to determine whether escape from aldosterone-mediated Na retention is associated with decreased abundance of one or more of renal Na transporters [10].
  • In this study, we used a proteomics approach to obtain further insight into the functional properties of nuclear beta-catenin [11].

Chemical compound and disease context of Proteomics


Biological context of Proteomics

  • To define the molecular mechanisms that govern this process during erythropoiesis, we have used tagging/proteomics approaches and characterized protein complexes nucleated by TAL-1/SCL, a basic helix-loop-helix transcription factor that specifies the erythrocytic lineage [17].
  • We were also able to observe the kinetics of substrate cleavage and cleavage product accumulation by using the 2D difference gel electrophoresis methodology. "Protease proteomics" may therefore represent an important tool for the discovery of the native substrates of a variety of proteases [18].
  • Our aim is to provide an overview of the physiology and genetics of nucleotide metabolism and its regulation that will facilitate the interpretation of data arising from genetics, metabolomics, proteomics, and transcriptomics in lactic acid bacteria [19].
  • It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics [20].
  • To elucidate possible mechanisms of this phenomenon, we used a proteomics approach and observed that levels of the proapoptotic protein, Bax, were increased following CTCF down-regulation in MCF7 cells [21].

Anatomical context of Proteomics


Associations of Proteomics with chemical compounds

  • Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics [26].
  • Can a proteomics strategy be used to identify the anti-malarial activity of chloroquine [27]?
  • Functional proteomics of nonalcoholic steatohepatitis: mitochondrial proteins as targets of S-adenosylmethionine [28].
  • A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter) [29].
  • These results show the potential of chemical proteomics to provide rationales for the development of potent kinase inhibitors, which combine rather unexpected biological modes of action by simultaneously targeting defined sets of both serine/threonine and tyrosine kinases involved in cancer progression [30].

Gene context of Proteomics

  • To investigate the molecular mechanisms of Hu functions, we used a proteomics strategy to isolate Hu-interacting proteins and identified heterogeneous nuclear ribonucleoprotein (hnRNP) K. hnRNP K also specifically binds to CU-rich sequences in p21 mRNA 3'-UTR and represses its translation in both nonneuronal and neuronal cells [31].
  • Using a proteomics approach, we have identified BAG2, a previously uncharacterized BAG domain-containing protein, as a common component of CHIP holocomplexes in vivo [32].
  • Using a two-dimensional gel-based proteomics approach we have also examined the scale of granzyme B-initiated alterations to the proteome in the presence or absence of effector caspase-3 or -7 [33].
  • Differential susceptibility of transferrin glycoforms to chymotrypsin: a proteomics approach to the detection of carbohydrate-deficient transferrin [34].
  • YML108W belongs to one of the numerous structural proteomics targets whose biological function is unknown [35].

Analytical, diagnostic and therapeutic context of Proteomics


  1. Down-regulation of mitochondrial F1F0-ATP synthase in human colon cancer cells with induced 5-fluorouracil resistance. Shin, Y.K., Yoo, B.C., Chang, H.J., Jeon, E., Hong, S.H., Jung, M.S., Lim, S.J., Park, J.G. Cancer Res. (2005) [Pubmed]
  2. Proteomic and functional analyses reveal a mitochondrial dysfunction in P301L tau transgenic mice. David, D.C., Hauptmann, S., Scherping, I., Schuessel, K., Keil, U., Rizzu, P., Ravid, R., Dröse, S., Brandt, U., Müller, W.E., Eckert, A., Götz, J. J. Biol. Chem. (2005) [Pubmed]
  3. Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication. Serva, S., Nagy, P.D. J. Virol. (2006) [Pubmed]
  4. Analysis of the quorum-sensing regulon of the opportunistic pathogen Burkholderia cepacia H111 by proteomics. Riedel, K., Arevalo-Ferro, C., Reil, G., Görg, A., Lottspeich, F., Eberl, L. Electrophoresis (2003) [Pubmed]
  5. Functional proteomics of breast cancer for signal pathway profiling and target discovery. Hondermarck, H., Dollé, L., El Yazidi-Belkoura, I., Vercoutter-Edouart, A.S., Adriaenssens, E., Lemoine, J. Journal of mammary gland biology and neoplasia. (2002) [Pubmed]
  6. Expression of the dihydropyrimidinase related protein 2 (DRP-2) in Down syndrome and Alzheimer's disease brain is downregulated at the mRNA and dysregulated at the protein level. Lubec, G., Nonaka, M., Krapfenbauer, K., Gratzer, M., Cairns, N., Fountoulakis, M. J. Neural Transm. Suppl. (1999) [Pubmed]
  7. MKS1, encoding a component of the flagellar apparatus basal body proteome, is mutated in Meckel syndrome. Kyttälä, M., Tallila, J., Salonen, R., Kopra, O., Kohlschmidt, N., Paavola-Sakki, P., Peltonen, L., Kestilä, M. Nat. Genet. (2006) [Pubmed]
  8. A phosphatase holoenzyme comprised of Shoc2/Sur8 and the catalytic subunit of PP1 functions as an M-Ras effector to modulate Raf activity. Rodriguez-Viciana, P., Oses-Prieto, J., Burlingame, A., Fried, M., McCormick, F. Mol. Cell (2006) [Pubmed]
  9. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Lewis, T.S., Hunt, J.B., Aveline, L.D., Jonscher, K.R., Louie, D.F., Yeh, J.M., Nahreini, T.S., Resing, K.A., Ahn, N.G. Mol. Cell (2000) [Pubmed]
  10. The renal thiazide-sensitive Na-Cl cotransporter as mediator of the aldosterone-escape phenomenon. Wang, X.Y., Masilamani, S., Nielsen, J., Kwon, T.H., Brooks, H.L., Nielsen, S., Knepper, M.A. J. Clin. Invest. (2001) [Pubmed]
  11. beta-catenin interacts with the FUS proto-oncogene product and regulates pre-mRNA splicing. Sato, S., Idogawa, M., Honda, K., Fujii, G., Kawashima, H., Takekuma, K., Hoshika, A., Hirohashi, S., Yamada, T. Gastroenterology (2005) [Pubmed]
  12. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Ruepp, S.U., Tonge, R.P., Shaw, J., Wallis, N., Pognan, F. Toxicol. Sci. (2002) [Pubmed]
  13. Enhanced detection and characterization of protocatechuate 3,4-dioxygenase in Acinetobacter lwoffii K24 by proteomics using a column separation. Kahng, H.Y., Cho, K., Song, S.Y., Kim, S.J., Leem, S.H., Kim, S.I. Biochem. Biophys. Res. Commun. (2002) [Pubmed]
  14. Acid-labile formylation of amino terminal proline of human immunodeficiency virus type 1 p24(gag) was found by proteomics using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Fuchigami, T., Misumi, S., Takamune, N., Takahashi, I., Takama, M., Shoji, S. Biochem. Biophys. Res. Commun. (2002) [Pubmed]
  15. Investigation of doxorubicin resistance in MCF-7 breast cancer cells using shot-gun comparative proteomics with proteolytic 18O labeling. Brown, K.J., Fenselau, C. J. Proteome Res. (2004) [Pubmed]
  16. Proteomics profile changes in cisplatin-treated human ovarian cancer cell strain. Li, Z., Zhao, X., Yang, J., Wei, Y. Sci. China, C, Life Sci. (2005) [Pubmed]
  17. ETO2 coordinates cellular proliferation and differentiation during erythropoiesis. Goardon, N., Lambert, J.A., Rodriguez, P., Nissaire, P., Herblot, S., Thibault, P., Dumenil, D., Strouboulis, J., Romeo, P.H., Hoang, T. EMBO J. (2006) [Pubmed]
  18. A proteomic approach for the discovery of protease substrates. Bredemeyer, A.J., Lewis, R.M., Malone, J.P., Davis, A.E., Gross, J., Townsend, R.R., Ley, T.J. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  19. Nucleotide metabolism and its control in lactic acid bacteria. Kilstrup, M., Hammer, K., Ruhdal Jensen, P., Martinussen, J. FEMS Microbiol. Rev. (2005) [Pubmed]
  20. Fragmentation pathways of protonated peptides. Paizs, B., Suhai, S. Mass spectrometry reviews. (2005) [Pubmed]
  21. Heightened expression of CTCF in breast cancer cells is associated with resistance to apoptosis. Docquier, F., Farrar, D., D'Arcy, V., Chernukhin, I., Robinson, A.F., Loukinov, D., Vatolin, S., Pack, S., Mackay, A., Harris, R.A., Dorricott, H., O'Hare, M.J., Lobanenkov, V., Klenova, E. Cancer Res. (2005) [Pubmed]
  22. Mitochondrial localization of estrogen receptor beta. Yang, S.H., Liu, R., Perez, E.J., Wen, Y., Stevens, S.M., Valencia, T., Brun-Zinkernagel, A.M., Prokai, L., Will, Y., Dykens, J., Koulen, P., Simpkins, J.W. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  23. Activation of antioxidant pathways in ras-mediated oncogenic transformation of human surface ovarian epithelial cells revealed by functional proteomics and mass spectrometry. Young, T.W., Mei, F.C., Yang, G., Thompson-Lanza, J.A., Liu, J., Cheng, X. Cancer Res. (2004) [Pubmed]
  24. Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire. Hoang, V.M., Foulk, R., Clauser, K., Burlingame, A., Gibson, B.W., Fisher, S.J. Biochemistry (2001) [Pubmed]
  25. The C terminus of lens aquaporin 0 interacts with the cytoskeletal proteins filensin and CP49. Lindsey Rose, K.M., Gourdie, R.G., Prescott, A.R., Quinlan, R.A., Crouch, R.K., Schey, K.L. Invest. Ophthalmol. Vis. Sci. (2006) [Pubmed]
  26. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Blagoev, B., Ong, S.E., Kratchmarova, I., Mann, M. Nat. Biotechnol. (2004) [Pubmed]
  27. Can a proteomics strategy be used to identify the anti-malarial activity of chloroquine? Petri, W.A. Trends Pharmacol. Sci. (2003) [Pubmed]
  28. Functional proteomics of nonalcoholic steatohepatitis: mitochondrial proteins as targets of S-adenosylmethionine. Santamaria, E., Avila, M.A., Latasa, M.U., Rubio, A., Martin-Duce, A., Lu, S.C., Mato, J.M., Corrales, F.J. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  29. A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts. Balmer, Y., Vensel, W.H., Cai, N., Manieri, W., Schürmann, P., Hurkman, W.J., Buchanan, B.B. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  30. Proteomic characterization of the angiogenesis inhibitor SU6668 reveals multiple impacts on cellular kinase signaling. Godl, K., Gruss, O.J., Eickhoff, J., Wissing, J., Blencke, S., Weber, M., Degen, H., Brehmer, D., Orfi, L., Horváth, Z., Kéri, G., Müller, S., Cotten, M., Ullrich, A., Daub, H. Cancer Res. (2005) [Pubmed]
  31. Involvement of Hu and heterogeneous nuclear ribonucleoprotein K in neuronal differentiation through p21 mRNA post-transcriptional regulation. Yano, M., Okano, H.J., Okano, H. J. Biol. Chem. (2005) [Pubmed]
  32. Regulation of the cytoplasmic quality control protein degradation pathway by BAG2. Dai, Q., Qian, S.B., Li, H.H., McDonough, H., Borchers, C., Huang, D., Takayama, S., Younger, J.M., Ren, H.Y., Cyr, D.M., Patterson, C. J. Biol. Chem. (2005) [Pubmed]
  33. Molecular ordering of the caspase activation cascade initiated by the cytotoxic T lymphocyte/natural killer (CTL/NK) protease granzyme B. Adrain, C., Murphy, B.M., Martin, S.J. J. Biol. Chem. (2005) [Pubmed]
  34. Differential susceptibility of transferrin glycoforms to chymotrypsin: a proteomics approach to the detection of carbohydrate-deficient transferrin. Valmu, L., Kalkkinen, N., Husa, A., Rye, P.D. Biochemistry (2005) [Pubmed]
  35. A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Pineda-Lucena, A., Liao, J.C., Cort, J.R., Yee, A., Kennedy, M.A., Edwards, A.M., Arrowsmith, C.H. Protein Sci. (2003) [Pubmed]
  36. Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. Venkatraman, A., Landar, A., Davis, A.J., Chamlee, L., Sanderson, T., Kim, H., Page, G., Pompilius, M., Ballinger, S., Darley-Usmar, V., Bailey, S.M. J. Biol. Chem. (2004) [Pubmed]
  37. MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports. Klenø, T.G., Andreasen, C.M., Kjeldal, H.Ø., Leonardsen, L.R., Krogh, T.N., Nielsen, P.F., Sørensen, M.V., Jensen, O.N. Anal. Chem. (2004) [Pubmed]
  38. Gamma-glutamylcysteine ethyl ester protection of proteins from Abeta(1-42)-mediated oxidative stress in neuronal cell culture: a proteomics approach. Boyd-Kimball, D., Sultana, R., Poon, H.F., Mohmmad-Abdul, H., Lynn, B.C., Klein, J.B., Butterfield, D.A. J. Neurosci. Res. (2005) [Pubmed]
  39. Next-generation protein-handling method: puromycin analogue technology. Tabuchi, I. Biochem. Biophys. Res. Commun. (2003) [Pubmed]
  40. Multiple site-directed mutagenesis of more than 10 sites simultaneously and in a single round. Seyfang, A., Jin, J.H. Anal. Biochem. (2004) [Pubmed]
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