title: Sample Preparation for Mass-Spectrometry Based Absolute Protein Quantification in Antibiotic Stress Research.
abstract: Absolute protein quantification is an essential tool for system biology approaches and elucidation of stoichiometry of multi-protein complexes. In this chapter, a universal protocol for gel free absolute protein quantification in bacterial systems is described, which can be used for sample preparation prior to miscellaneous mass-spectrometry-based quantification workflows like AQUA, Hi3, and emPAI. In addition, a focus has been set to the specific challenges in antibiotic stress research.
authors.affiliation: Department for Microbial Proteomics, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, Greifswald, 17489, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Bonn
authors.affiliation: Department for Microbial Proteomics, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, Greifswald, 17489, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Maass
authors.affiliation: Department for Microbial Proteomics, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, Greifswald, 17489, Germany. dbecher@uni-greifswald.de.
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000032:analysis*; D002458:Cell Fractionation; D015169:Colony Count, Microbial; D013058:Mass Spectrometry / Q000379:methods*; D013312:Stress, Physiological; D014357:Trypsin / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D014357:Trypsin
keywords: AQUA; Absolute protein quantification; Antibiotic stress response; Gel free proteomics; Hi3; In-solution digestion; QconCAT; Sample preparation; emPAI