title: SILAC yeast: from labeling to comprehensive proteome quantification.
abstract: Mass spectrometry-based quantitative proteomics can identify and quantify thousands of proteins in complex mixtures, enabling characterization and comparison of cellular functional states in a proteome-wide scale. In this context, stable isotope labeling with amino acids in cell culture (SILAC) has emerged as a simple yet powerful approach, which has been applied to address different biological questions across a variety of systems, ranging from single cells to entire multicellular organisms. In this chapter, detailed instructions for SILAC labeling yeast are provided, including a series of quality checks for evaluating labeling efficiency and procedures for determining the optimal labeling parameters for a particular yeast strain. In addition, two different complete workflows for the comprehensive mass spectrometry-based SILAC quantification of close to the entire yeast proteome are described, which can be applied to assess any biological question of interest and, therefore, can be of broad use for the researchers in the field.
authors.affiliation: Instituto Carlos Chagas, Fiocruz Parana, Rua Prof. Algacyr Munhoz Mader 3775, 81350-010, Curitiba, PR, Brazil, lmfgodoy@fiocruz.br.
authors.forename: Lyris M F
authors.initials: LM
authors.lastname: de Godoy
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D056148:Chromatography, Reverse-Phase; D004591:Electrophoresis, Polyacrylamide Gel; D005656:Fungal Proteins / Q000737:chemistry*; D007525:Isoelectric Focusing; D007553:Isotope Labeling; D008969:Molecular Sequence Data; D020543:Proteome; D053719:Tandem Mass Spectrometry / Q000379:methods*; D015003:Yeasts / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D005656:Fungal Proteins; D020543:Proteome