Abstract: The invention relates generally to peptide biomarkers with specific ionization characteristics to directly quantify one or more transgenic target proteins in biological samples, including transgenic plant samples, by liquid chromatography coupled tandem mass spectrometry multiple reaction monitoring (MRM). The peptide biomarkers in combination with MRM-based methods may be used to quantify a single transgenic target protein or multiple transgenic target proteins within a stacked transgenic crop, such as maize, utilizing selected peptide biomarkers either alone or in combination. The present disclosure allows for broad based, reliable quantitation in different biological matrices, including plant matrices. The peptide biomarkers of the invention can further be used as trait biomarkers to support identification and/or selection of specific transgenic Events. Also provided are different peptide biomarker combinations that can be used to perform the methods of the invention.

Abstract: Systems, methods, computer programming product, and databases for virtual mass spectrometry (VMS) enable the identification of polypeptides in samples without acquisition of MS/MS fragmentation spectra. Methods according to the invention employ databases containing records corresponding to polypeptides potentially present in samples. In addition to identifying polypeptides, such databases may be used for other purposes, including for example to correct experimental data, e.g., for analytical systemic errors.