Science China Life Sciences

, Volume 61, Issue 3, pp 351–354 | Cite as

Towards a one-stop solution for large-scale proteomics data analysis

  • Yi Zhu
  • Tiannan Guo


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  1. Bell, A.W., Deutsch, E.W., Au, C.E., Kearney, R.E., Beavis, R., Sechi, S., Nilsson, T., Bergeron, J.J., and Group, H.T.S.W. (2009). A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 6, 423–430.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Cox, J., and Mann, M. (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367–1372.CrossRefPubMedGoogle Scholar
  3. Cyranoski, D. (2010). China pushes for the proteome. Nature 467, 380.CrossRefPubMedGoogle Scholar
  4. Deutsch, E.W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J.K., Martin, D.B., Nesvizhskii, A.I., and Aebersold, R. (2010). A guided tour of the Trans-Proteomic Pipeline. Proteomics 10, 1150–1159.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Feng, J., Ding, C., Qiu, N., Ni, X., Zhan, D., Liu, W., Xia, X., Li, P., Lu, B., Zhao, Q., Nie, P., Song, L., Zhou, Q., Lai, M., Guo, G., Zhu, W., Ren, J., Shi, T., and Qin, J. (2017). Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. Nat Biotechnol 35, 409–412.CrossRefPubMedGoogle Scholar
  6. MacLean, B., Tomazela, D.M., Shulman, N., Chambers, M., Finney, G.L., Frewen, B., Kern, R., Tabb, D.L., Liebler, D.C., and MacCoss, M.J. (2010). Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Ori, A., Iskar, M., Buczak, K., Kastritis, P., Parca, L., Andres-Pons, A., Singer, S., Bork, P., and Beck, M. (2016). Spatiotemporal variation of mammalian protein complex stoichiometries. Genome Biol 17, 47.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Riley, N.M., Hebert A.S., and Coon, J.J. (2016). Proteomics Moves into the Fast Lane. Cell Syst 2, 142–143.CrossRefPubMedGoogle Scholar
  9. Slagel, J., Mendoza, L., Shteynberg, D., Deutsch, E.W., and Moritz, R.L. (2015). Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. Mol Cell Proteomics 14, 399–404.CrossRefPubMedGoogle Scholar
  10. Vizcaino, J.A., Csordas, A., del-Toro, N., Dianes, J.A., Griss, J., Lavidas, I., Mayer, G., Perez-Riverol, Y., Reisinger, F., Ternent, T., Xu, Q., Wang, R., and Hermjakob, H. (2016). 2016 update of the PRIDE database and its related tools. Nucleic Acids Res 44, D447–456CrossRefPubMedGoogle Scholar

Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouChina
  2. 2.Westlake UniversityHangzhouChina

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