This chapter describes the most common methods that do not rely on the combination of liquid chromatography and mass spectrometry. In general, 2D SDS-PAGE gel quantification is based on the signal intensity of the spot in which the protein has been found. A widely used technique to avoid the typical low reproducibility between different gels is the fluorescence-based differential in-gel electrophoresis (DIGE) approach. Another often-used method for discovery oriented protein quantification is provided by protein arrays. Where 2D gel electrophoresis and protein arrays provide discovery oriented methods used to detect and quantify as many proteins as possible in a sample,Western blotting provides a targeted means to quantify a single protein in a sample. Another popular means of targeted protein quantification is offered by enzyme-linked immunosorbent assay (ELISA). ELISA is often used in clinical assays, and the development of an ELISA is therefore often the endpoint of a biomarker discovery pipeline. Controlled Vocabulary Terms Computational statistics; Inferential statistics

Post-translational modifications (PTMs) are crucial for the heterogeneity of proteins. PTMs are often used to regulate how proteins will act in eukaryotic organisms; disregulation of PTMs is important in many diseases. Examining how the extent of modifications varies over different situations is therefore interesting from both a basic biological as well as from a clinical perspective. Although mass spectrometry has been applied to the quantification of PTMs for more than ten years, there are essentially no general methods available that can analyze all types of modifications. Absolute modification degrees have to be calculated from the observed abundances. Relative modification degree can be calculated from absolute modification degrees. The chapter also discusses discovery based modification stoichiometry. Controlled Vocabulary Terms Computational statistics Inferential statistics

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

This chapter contains sections titled: Units of Structure Descriptions Coordinates Distance Matrices Torsion Angles Coarse Level Description Identifying the SSEs Structure Comparison Framework for Pairwise Structure Comparison Exercises Bibliographic notes