Statistical methods for quantitative mass spectrometry proteomic experiments with labeling

In this manuscript we focus on statistical methods for quantitative mass spectrometry (MS) based proteomic experiments as they pertain to labeling protocols. Labeling of fragmented proteins (i.e., peptides) allows specimens to be labeled without altering the chemical properties of the peptides, mixed into a single aliquot and then subjected to MS simultaneously. The advantage of the labeling protocol is that specimens can be distinguished in the resulting data by leveraging known properties of the labels. For example, if stable isotopes are used, the known mass shift resulting from extra neutrons together with known naturally occurring distributions of isotopes in the atmosphere are used during the relative quantification step.