1. A method of detecting a polypeptide of interest in a plant without the use of a reference standard, said method comprising: (a) obtaining a plant wherein the expression of said polypeptide of interest is suppressed and a negative control plant that does express said polypeptide of interest; (b) preparing a sample from said plant and a negative control sample from said negative control plant for analysis; and (c) determining whether an MRM transition signal associated with identified tryptic peptides for the polypeptide of interest is present at a determined retention time in LC-MRM ion chromatograms of said sample and said negative control sample; wherein the presence of an MRM transition signal at said determined retention time in said negative control sample, and the absence of a corresponding MRM transition signal in said sample, indicates the absence of said polypeptide of interest in said plant.