Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry

Abstract

The adaptation of sequences of chemical reactions to a solid-phase format has been essential to the automation, reproducibility, and efficiency of a number of biotechnological processes including peptide and oligonucleotide synthesis and sequencing1,2,3,4. Here we describe a method for the site-specific, stable isotopic labeling of cysteinyl peptides in complex peptide mixtures through a solid-phase capture and release process, and the concomitant isolation of the labeled peptides. The recovered peptides were analyzed by microcapillary liquid chromatography and tandem mass spectrometry (μLC-MS/MS) to determine their sequences and relative quantities. The method was used to detect galactose-induced changes in protein abundance in the yeast Saccharomyces cerevisiae. A side-by-side comparison with the isotope-coded affinity tag (ICAT) method5 demonstrated that the solid-phase method for stable isotope tagging of peptides is comparatively simpler, more efficient, and more sensitive.

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Figure 1: Schematic representation of the solid-phase isotope tagging method.
Figure 2: Validation of the solid-phase capture and release method.
Figure 3: Summary of the number of proteins identified and quantified by the solid-phase and ICAT methods.

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Acknowledgements

This work was supported in part by the US National Cancer Institute grant (CA84698), National Institutes of Health (NIH) Research Resource Center (RR11823), NIH grant (GM 41109) to R.A., and NIH postdoctoral fellowship (GM19884) to J.A.R.

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Correspondence to Ruedi Aebersold.

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Zhou, H., Ranish, J., Watts, J. et al. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol 20, 512–515 (2002). https://doi.org/10.1038/nbt0502-512

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