Proteomics seeks to monitor the flux of protein through a biological system under variable developmental and environmental influences as programmed by the genome but, if it is to deliver its true potential, it is critically important that our proteomics technologies deliver reproducible quantitation. Because of the variability of day-to-day measurements of protein quantities, a common feature of quantitative proteomics is the use of stable isotope coding to distinguish control and experimental samples in a mixture that can be profiled in a single experiment. Coding with stable isotopes can be achieved by growth of an organism in depleted/enriched media, or by chemically modifying proteins after extraction from the organism, though these later approaches are not useful for measurement of protein turnover rates. Current stable isotope strategies seek full isotope- exchange, that is, to swap all 14N for 15N, 12C for 13C, or 16O for 18O, such that a peptide's mass is altered by several Daltons. These methods are expensive, because of the need for high isotope purity, and it was estimated that the first 15N rat cost ~$10,000. Furthermore, the fact that two peptide isotopomer distributions replace one leads to a practical loss of separation space in the mass spectrometer demanding more efficient peptide separations. Moreover, the second isotopomer distribution may trigger MS-MS in automated proteomics experiments, wasting mass spectrometer time. If a particular protein has been massively up-or-down-regulated there is also the possibility that its presence will be ignored because there weren't any readily identified pairs of peptide signals in the mass spectrum. We propose here an inexpensive strategy, potentially applicable to expression proteomics and turnover measurements in living humans, that codes the quantitative differential expression information within a single isotopomer envelope.
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