Label Based Quantification by MS Spectra

Label based quantification by MS spectra consists of two main steps: Quantification by MS spectra and identification by MS/MS spectra. The main principle for the quantification is straightforward: (i) the samples to be compared are modified using labels that have the same chromatographic characteristics, thus ensuring that the different versions of a peptide occur in the same MS spectra; (ii) the masses of the labels and the charge of the peptide are then used to locate variants of the same peptide in an MS spectrum. This chapter discusses various labeling techniques such as: metabolic labeling — SILAC (Stable Isotope Labeling with Amino acids in Cell culture), chemical labeling and enzymatic labeling. The peaks that can be used for quantification depend largely on the peaks that are selected for MS/MS processing. The chapter describes label based quantification by MS spectra based on how this procedure is handled by MaxQuant. Controlled Vocabulary Terms Computational statistics; Inferential statistics