Advertisement

Shared Peptides in Mass Spectrometry Based Protein Quantification

  • Banu Dost
  • Nuno Bandeira
  • Xiangqian Li
  • Zhouxin Shen
  • Steve Briggs
  • Vineet Bafna
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)

Abstract

In analyzing the proteome using mass spectrometry, the mass values help identify the molecules, and the intensities help quantify them, relative to their abundance in other samples. Peptides that are shared across different protein sequences are typically discarded as being uninformative w.r.t each of the parent proteins.

In this paper, we investigate the use of shared peptides which are ubiquitous (~50% of peptides) in mass spectrometric data-sets. In many cases, shared peptides can help compute the relative amounts of different proteins that share the same peptide. Also, proteins with no unique peptide in the sample can still be analyzed for relative abundance. Our paper is the first attempt to use shared peptides in protein quantification, and makes use of combinatorial optimization to reduce the error in relative abundance measurements. We describe the topological and numerical properties required for robust estimates, and use them to improve our estimates for ill-conditioned systems. Extensive simulations validate our approach even in the presence of experimental error. We apply our method to a model of Arabidopsis root knot nematode infection, and elucidate the differential role of many protein family members in mediating host response to the pathogen.

Keywords

shared peptides protein quantification linear programming optimization ITRAQ mass spectrometry 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Alves, P., Arnold, R.J., Novotny, M.V., Radivojac, P., Reilly, J.P., Tang, H.: Advancement in protein inference from shotgun proteomics using peptide detectability. In: Pac. Symp. Biocomput., pp. 409–420 (2007)Google Scholar
  2. 2.
    Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B.: Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389(4), 1017–1031 (2007)CrossRefPubMedGoogle Scholar
  3. 3.
    An Advanced Treatise on Meloidogyne: Volume I. North Carolina State University Graphics (1985)Google Scholar
  4. 4.
    Jammes, F., Lecomte, P., de Almeida-Engler, J., Bitton, F., Martin-Magniette, M.L., Renou, J.P., Abad, P., Favery, B.: Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. The Plant Journal 44, 447–458 (2005)CrossRefPubMedGoogle Scholar
  5. 5.
    Jeong, Y.M., Mun, J.H., Lee, I., Woo, J.C., Hong, C.B., Kim, S.G.: Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members. Plant Physiol. 140, 196–209 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Jones, A.M., Bennett, M.H., Mansfield, J.W., Grant, M.: Analysis of the defence phosphoproteome of arabidopsis thaliana using differential mass tagging. Proteomics 6(14), 4155–4165 (2006)CrossRefPubMedGoogle Scholar
  7. 7.
    Kim, S.J., Kim, K.W., Cho, M.H., Franceschi, V.R., Davin, L.B., Lewis, N.G.: Expression of cinnamyl alcohol dehydrogenases and their putative homologues during Arabidopsis thaliana growth and development: lessons for database annotations?. Phytochemistry 68, 1957–1974 (2007)CrossRefPubMedGoogle Scholar
  8. 8.
    Mallick, P., Schirle, M., Chen, S.S., Flory, M.R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., Aebersold, R.: Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25(1), 125–131 (2007)CrossRefPubMedGoogle Scholar
  9. 9.
    Marmagne, A., Rouet, M.A., Ferro, M., Rolland, N., Alcon, C., Joyard, J., Garin, J., Barbier-Brygoo, H., Ephritikhine, G.: Identification of new intrinsic proteins in Arabidopsis plasma membrane proteome. Mol. Cell Proteomics 3, 675–691 (2004)CrossRefPubMedGoogle Scholar
  10. 10.
  11. 11.
    Wiese, S., Reidegeld, K.A., Meyer, H.E., Warscheid, B.: Protein labeling by itraq: a new tool for quantitative mass spectrometry in proteome research. Proteomics 7(3), 340–350 (2007)CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Banu Dost
    • 1
  • Nuno Bandeira
    • 1
  • Xiangqian Li
    • 2
  • Zhouxin Shen
    • 2
  • Steve Briggs
    • 2
  • Vineet Bafna
    • 1
  1. 1.Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoUSA
  2. 2.Department of Biological SciencesUniversity of CaliforniaSan DiegoUSA

Personalised recommendations