title: Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation.
abstract: The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response.
authors.affiliation: Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany.
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.forename: Martin
authors.initials: M
authors.lastname: Taubert
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.forename: Tobias
authors.initials: T
authors.lastname: Behr
authors.forename: Frank
authors.initials: F
authors.lastname: Schmidt
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D001673:Biodegradation, Environmental; D004785:Environmental Pollutants / Q000378:metabolism*; D007553:Isotope Labeling; D009281:Naphthalenes / Q000378:metabolism*; D040901:Proteomics; D011551:Pseudomonas fluorescens / Q000378:metabolism*; D013460:Sulfur Isotopes
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D004785:Environmental Pollutants; D009281:Naphthalenes; D013460:Sulfur Isotopes; C031721:naphthalene