Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

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Abstract
A mass spectrometry instrument control method—QuantMode—allows accurate, large-scale, multiplexed quantitative proteomics measurements using isobaric tagging by removing the problem of precursor interference. Also in this issue, Ting et al. provide a different solution to the same problem. We describe a mass spectrometry method, QuantMode, which improves accuracy of isobaric tag–based quantification by alleviating the pervasive problem of precursor interference, simultaneous isolation and fragmentation of impurities, through gas-phase purification. QuantMode analysis of a yeast sample 'contaminated' with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan, with a small loss of spectral identifications. This technique enables large-scale, multiplexed quantitative proteomics using isobaric tagging.