Computational Biology pp 211-222

Part of the Methods in Molecular Biology book series (MIMB, volume 673)

Protein Quantitation Using Mass Spectrometry

  • Guoan Zhang
  • Beatrix M. Ueberheide
  • Sofia Waldemarson
  • Sunnie Myung
  • Kelly Molloy
  • Jan Eriksson
  • Brian T. Chait
  • Thomas A. Neubert
  • David Fenyö
Protocol

Abstract

Mass spectrometry is a method of choice for quantifying low-abundance proteins and peptides in many biological studies. Here, we describe a range of computational aspects of protein and peptide quantitation, including methods for finding and integrating mass spectrometric peptide peaks, and detecting interference to obtain a robust measure of the amount of proteins present in samples.

Key words

Proteomics Quantitation Proteins Peptides Mass spectrometry 

References

  1. 1.
    Y. Oda, K. Huang, F.R. Cross, D. Cowburn, and B.T. Chait (1999) Accurate quantitation of protein expression and site-specific phosphorylation, Proc Natl Acad Sci USA, 96, 6591–6.PubMedCrossRefGoogle Scholar
  2. 2.
    S.E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol Cell Proteomics, 1, 376–86.PubMedCrossRefGoogle Scholar
  3. 3.
    B. Schwanhausser, M. Gossen, G. Dittmar, and M. Selbach (2009) Global analysis of cellular protein translation by pulsed SILAC, Proteomics, 9, 205–9.PubMedCrossRefGoogle Scholar
  4. 4.
    S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags, Nat Biotechnol, 17, 994–9.PubMedCrossRefGoogle Scholar
  5. 5.
    O.A. Mirgorodskaya, Y.P. Kozmin, M.I. Titov, R. Korner, C.P. Sonksen, and P. Roepstorff (2000) Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18)O-labeled internal standards, Rapid Commun Mass Spectrom, 14, 1226–32.PubMedCrossRefGoogle Scholar
  6. 6.
    S.A. Gerber, J. Rush, O. Stemman, M.W. Kirschner, and S.P. Gygi (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS, Proc Natl Acad Sci USA, 100, 6940–5.PubMedCrossRefGoogle Scholar
  7. 7.
    P.L. Ross, Y.N. Huang, J.N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, F. He, A. Jacobson, and D.J. Pappin (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol Cell Proteomics, 3, 1154–69.PubMedCrossRefGoogle Scholar
  8. 8.
    R.J. Beynon, M.K. Doherty, J.M. Pratt, and S.J. Gaskell (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides, Nat Methods, 2, 587–9.PubMedCrossRefGoogle Scholar
  9. 9.
    L. Anderson and C.L. Hunter (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins, Mol Cell Proteomics, 5, 573–88.PubMedGoogle Scholar
  10. 10.
    E.C. Yi, X.J. Li, K. Cooke, H. Lee, B. Raught, A. Page, V. Aneliunas, P. Hieter, D.R. Goodlett, and R. Aebersold (2005) Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme, Proteomics, 5, 380–7.PubMedCrossRefGoogle Scholar
  11. 11.
    P. Schulz-Knappe, H.D. Zucht, G. Heine, M. Jurgens, R. Hess, and M. Schrader (2001) Peptidomics: the comprehensive analysis of peptides in complex biological mixtures, Comb Chem High Throughput Screen, 4, 207–17.PubMedCrossRefGoogle Scholar
  12. 12.
    W. Wang, H. Zhou, H. Lin, S. Roy, T.A. Shaler, L.R. Hill, S. Norton, P. Kumar, M. Anderle, and C.H. Becker (2003) Quan­tification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards, Anal Chem, 75, 4818–26.PubMedCrossRefGoogle Scholar
  13. 13.
    M.C. Wiener, J.R. Sachs, E.G. Deyanova, and N.A. Yates (2004) Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures, Anal Chem, 76, 6085–96.PubMedCrossRefGoogle Scholar
  14. 14.
    T.A. Addona, S.E. Abbatiello, B. Schilling, S.J. Skates, D.R. Mani, D.M. Bunk, C.H. Spiegelman, L.J. Zimmerman, A.J. Ham, H. Keshishian, S.C. Hall, S. Allen, R.K. Blackman, C.H. Borchers, C. Buck, H.L. Cardasis, M.P. Cusack, N.G. Dodder, B.W. Gibson, J.M. Held, T. Hiltke, A. Jackson, E.B. Johansen, C.R. Kinsinger, J. Li, M. Mesri, T.A. Neubert, R.K. Niles, T.C. Pulsipher, D. Ransohoff, H. Rodriguez, P.A. Rudnick, D. Smith, D.L. Tabb, T.J. Tegeler, A.M. Variyath, L.J. Vega-Montoto, A. Wahlander, S. Waldemarson, M. Wang, J.R. Whiteaker, L. Zhao, N.L. Anderson, S.J. Fisher, D.C. Liebler, A.G. Paulovich, F.E. Regnier, P. Tempst, and S.A. Carr (2009) Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma, Nat Biotechnol, 27, 633–41.PubMedCrossRefGoogle Scholar
  15. 15.
    H. Liu, R.G. Sadygov, and J.R. Yates, 3rd (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics, Anal Chem, 76, 4193–201.PubMedCrossRefGoogle Scholar
  16. 16.
    Y. Ishihama, Y. Oda, T. Tabata, T. Sato, T. Nagasu, J. Rappsilber, and M. Mann (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein, Mol Cell Proteomics, 4, 1265–72.PubMedCrossRefGoogle Scholar
  17. 17.
    X.J. Li, H. Zhang, J.A. Ranish, and R. Aebersold (2003) Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry, Anal Chem, 75, 6648–57.PubMedCrossRefGoogle Scholar
  18. 18.
    J. Cox and M. Mann (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat Biotechnol, 26, 1367–72.PubMedCrossRefGoogle Scholar
  19. 19.
    J. Cox, I. Matic, M. Hilger, N. Nagaraj, M. Selbach, J.V. Olsen, and M. Mann (2009) A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics, Nat Protoc, 4, 698–705.PubMedCrossRefGoogle Scholar
  20. 20.
    P. Mortensen, J.W. Gouw, J.V. Olsen, S.E. Ong, K.T. Rigbolt, J. Bunkenborg, J. Cox, L.J. Foster, A.J. Heck, B. Blagoev, J.S. Andersen, and M. Mann (2010) MSQuant, an open source platform for mass spectrometry-based quantitative proteomics, J Proteome Res, 9(1):393–403.PubMedCrossRefGoogle Scholar
  21. 21.
    Z. Khan, J.S. Bloom, B.A. Garcia, M. Singh, and L. Kruglyak (2009) Protein quantification across hundreds of experimental conditions, Proc Natl Acad Sci USA, 106, 15544–8.PubMedCrossRefGoogle Scholar
  22. 22.
    A.M. Boehm, S. Putz, D. Altenhofer, A. Sickmann, and M. Falk (2007) Precise protein quantification based on peptide quantification using iTRAQ, BMC Bioinformatics, 8, 214.PubMedCrossRefGoogle Scholar
  23. 23.
    C.J. Mason, T.M. Therneau, J.E. Eckel-Passow, K.L. Johnson, A.L. Oberg, J.E. Olson, K.S. Nair, D.C. Muddiman, and H.R. Bergen, 3rd (2007) A method for automatically interpreting mass spectra of 18O-labeled isotopic clusters, Mol Cell Proteomics, 6, 305–18.PubMedGoogle Scholar
  24. 24.
    B. MacLean, D.M. Tomazela, N. Shulman, M. Chambers, G. Finney, B. Frewen, R. Kern, D.L. Tabb, D.C. Liebler and M.J. Maccoss (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966–8.Google Scholar
  25. 25.
    E.M. Woo, D. Fenyo, B.H. Kwok, H. Funabiki, and B.T. Chait (2008) Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting, Anal Chem, 80, 2419–25.PubMedCrossRefGoogle Scholar
  26. 26.
    G. Zhang, D. Fenyo, and T.A. Neubert (2009) Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture, J Proteome Res, 8, 1285–92.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Guoan Zhang
    • 1
  • Beatrix M. Ueberheide
    • 2
  • Sofia Waldemarson
    • 1
  • Sunnie Myung
    • 2
  • Kelly Molloy
    • 2
  • Jan Eriksson
    • 3
  • Brian T. Chait
    • 2
  • Thomas A. Neubert
    • 1
  • David Fenyö
    • 2
  1. 1.Kimmel Center for Biology and Medicine at the Skirball Institute and Department of PharmacologyNew York University School of MedicineNew YorkUSA
  2. 2.The Rockefeller UniversityNew YorkUSA
  3. 3.Department of ChemistrySwedish University of Agricultural SciencesUppsalaSweden

Personalised recommendations