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Neutron-Encoded Protein Quantification by Peptide Carbamylation

  • Arne Ulbrich
  • Anna E. Merrill
  • Alexander S. Hebert
  • Michael S. Westphall
  • Mark P. Keller
  • Alan D. Attie
  • Joshua J. CoonEmail author
Short Communication

Abstract

We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression in mice fed a either control or high-fat diet.

Key words

Quantitative proteomics NeuCode FTMS Chemical label Isobaric tag Mass defect 

Notes

Acknowledgments

This work was supported by the National Institutes of Health grants R01 DK066369, DK058037 and DK091207 (A.D.A.), and GM080148 (J.J.C.). A.E.M. gratefully acknowledges support from a National Institutes of Health-funded Genomic Sciences Training Program (5T32HG002760).

Supplementary material

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References

  1. 1.
    Hebert, A.S., Merrill, A.E., Bailey, D.J., Still, A.J., Westphall, M.S., Strieter, E.R., Pagliarini, D.J., Coon, J.J.: Neutron-encoded mass signatures for multiplexed proteome quantification. Nat. Methods 10, 332–334 (2013)Google Scholar
  2. 2.
    Sleno, L.: The use of mass defect in modern mass spectrometry. J. Mass Spectrom. 47, 226–236 (2012)CrossRefGoogle Scholar
  3. 3.
    Alvarez-Manilla, G., Warren, N.L., Abney, T., Atwood, J., Azadi, P., York, W.S., Pierce, M., Orlando, R.: Tools for glycomics: relative quantitation of glycans by isotopic permethylation using (CH3I)-C-13. Glycobiology 17, 677–687 (2007)CrossRefGoogle Scholar
  4. 4.
    Vincent, C.E., Potts, G.K., Ulbrich, A., Westphall, M.S., Atwood, J.A., Coon, J.J., Weatherly, D.B.: Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantification. Anal. Chem. 85, 2825–2832 (2013)CrossRefGoogle Scholar
  5. 5.
    Hebert, A.S., Dittenhafer-Reed, K.E., Yu, W., Bailey, D.J., Selen, E.S., Boersma, M.D., Carson, J.J., Tonelli, M., Balloon, A.J., Higbee, A.J., Westphall, M.S., Pagliarini, D.J., Prolla, T.A., Assadi-Porter, F., Roy, S., Denu, J.M., Coon, J.J.: Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol. Cell 49, 186–199 (2013)Google Scholar
  6. 6.
    Angel, P.M., Orlando, R.: Quantitative carbamylation as a stable isotopic labeling method for comparative proteomics. Rapid Commun. Mass Spectrom. 21, 1623–1634 (2007)CrossRefGoogle Scholar
  7. 7.
    Elias, J.E., Gygi, S.P.: Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007)CrossRefGoogle Scholar
  8. 8.
    Geer, L.Y., Markey, S.P., Kowalak, J.A., Wagner, L., Xu, M., Maynard, D.M., Yang, X., Shi, W., Bryant, S.H.: Open mass spectrometry search algorithm. J. Proteome Res. 3, 958–964 (2004)CrossRefGoogle Scholar
  9. 9.
    Wenger, C.D., Phanstiel, D.H., Lee, M.V., Bailey, D.J., Coon, J.J.: COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics 11, 1064–1074 (2011)CrossRefGoogle Scholar
  10. 10.
    Denisov, E., Damoc, E., Lange, O., Makarov, A.: Orbitrap mass spectrometry with resolving powers above 1,000,000. Int. J. Mass Spectrom. 325, 80–85 (2012)CrossRefGoogle Scholar
  11. 11.
    Swaney, D.L., Wenger, C.D., Coon, J.J.: Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9, 1323–1329 (2010)CrossRefGoogle Scholar
  12. 12.
    Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B.: Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389, 1017–1031 (2007)CrossRefGoogle Scholar
  13. 13.
    Kozawa, S., Honda, A., Kajiwara, N., Takemoto, Y., Nagase, T., Nikami, H., Okano, Y., Nakashima, S., Shimozawa, N.: Induction of peroxisomal lipid metabolism in mice fed a high-fat diet. Mol. Med. Rep. 4, 1157–1162 (2011)Google Scholar
  14. 14.
    Sparks, L.M., Xie, H., Koza, R.A., Mynatt, R., Hulver, M.W., Bray, G.A., Smith, S.R.: A high-fat diet coordinately downregulates genes required for mitochondrial oxidative phosphorylation in skeletal muscle. Diabetes 54, 1926–1933 (2005)CrossRefGoogle Scholar
  15. 15.
    Huang, D.W., Sherman, B.T., Lempicki, R.A.: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2013

Authors and Affiliations

  • Arne Ulbrich
    • 1
    • 3
  • Anna E. Merrill
    • 1
    • 3
  • Alexander S. Hebert
    • 2
    • 3
  • Michael S. Westphall
    • 3
  • Mark P. Keller
    • 4
  • Alan D. Attie
    • 4
  • Joshua J. Coon
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of ChemistryUniversity of WisconsinMadisonUSA
  2. 2.Department of Biomolecular ChemistryUniversity of WisconsinMadisonUSA
  3. 3.Genome Center of WisconsinUniversity of WisconsinMadisonUSA
  4. 4.Department of BiochemistryUniversity of WisconsinMadisonUSA

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