The PEAKS development team has developed a solution to address MultiNotch MS3 Quantitation, currently in use by Proteome Sciences for biomarker discovery. MS3 provides more accurate quantification for isobaric tagging experiments, specifically improving TMT and iTRAQ based studies.
In 2011, Gygi et al. reported isobaric labeling mass spectrometry–based proteome quantification commonly suffers ratio distortion owing to protein quantification interference.1 A more recent publication by the authors identifies that the combination of quantitative isobaric reagents and the MultiNotch MS3 method improves the dynamic range of reporter ion quantitation, reducing reporter ion signal variance, and ultimately produces more high-quality quantitative measurement.2 Our development team implemented a data analysis solution to address these points in order to generate more sensitive and accurate results for end users.
The MultiNotch MS3 quantitation solution is currently in use by Proteome Sciences.