Abstract
Quantitative proteome profiling of microorganisms by isotopic labeling of amino acids is still a challenge, because only microorganisms with auxotrophic character are able to embed amino acids into their biomass in a quantitatively correct manner. Here, we describe an isotopic labeling technique (sulfur stable isotope labeling of amino acids for quantification, SULAQ) for the sulfur-containing amino acids cysteine and methionine in a broad range of organisms. The metabolic labeling approach is suitable for gel-based and gel-free protein analysis.
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References
Bachi A, Bonaldi T (2008) Quantitative proteomics as a new piece of the systems biology puzzle. J Proteome 71(3):357–367
Ong SE, Mann M (2005) Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 1(5):252–262
Chen X, Sun L, Yu Y, Xue Y, Yang P (2007) Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics 4(1):25–37
Filiou MD, Varadarajulu J, Teplytska L, Reckow S, Maccarrone G, Turck CW (2012) The 15N isotope effect in Escherichia coli: a neutron can make the difference. Proteomics 12(21):3121–3128
Hoedt E, Zhang G, Neubert TA (2014) Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. Adv Exp Med Biol 806:93–106
Matthes A, Kohl K, Schulze WX (2014) SILAC and alternatives in studying cellular proteomes of plants. Methods Mol Biol 1188:65–83
Petriz BA, Franco OL (2014) Application of cutting-edge proteomics technologies for elucidating host-bacteria interactions. Adv Protein Chem Struct Biol 95:1–24
Schmidt F, Volker U (2011) Proteome analysis of host-pathogen interactions: Investigation of pathogen responses to the host cell environment. Proteomics 11(15):3203–3211
Muller SA, Pernitzsch SR, Haange SB, Uetz P, von Bergen M, Sharma CM, Kalkhof S (2015) Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori. J Proteome 126:34–45
Oda Y, Huang K, Cross FR, Cowburn D, Chait BT (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 96(12):6591–6596
Snijders AP, de Koning B, Wright PC (2005) Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics. J Proteome Res 4(6):2185–2191
Jehmlich N, Schmidt F, Hartwich M, von Bergen M, Richnow HH, Vogt C (2008) Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Commun Mass Spectrom 22(18):2889–2897
Jehmlich N, Kopinke FD, Lenhard S, Vogt C, Herbst FA, Seifert J, Lissner U, Volker U, Schmidt F, von Bergen M (2012) Sulfur-36S stable isotope labeling of amino acids for quantification (SULAQ). Proteomics 12(1):37–42
Herbst FA, Taubert M, Jehmlich N, Behr T, Schmidt F, von Bergen M, Seifert J (2013) Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation. Mol Cell Proteomics 12(8):2060–2069
Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24(21):2534–2536
Hoopmann MR, MacCoss MJ, Moritz RL (2012) Identification of peptide features in precursor spectra using Hardklor and Kronik. Curr Protoc Bioinformatics Chapter 13:Unit13 18
Otto A, Bernhardt J, Meyer H, Schaffer M, Herbst FA, Siebourg J, Mader U, Lalk M, Hecker M, Becher D (2010) Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis. Nat Commun 1:137
Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1(6):2856–2860
Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2(8):1896–1906
Chen D, Shah A, Nguyen H, Loo D, Inder KL, Hill MM (2014) Online quantitative proteomics p-value calculator for permutation-based statistical testing of peptide ratios. J Proteome Res 13(9):4184–4191
Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 13(9):731–740
Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57
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Herbst, FA., Jehmlich, N., von Bergen, M., Schmidt, F. (2018). Sulfur-34S and 36S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34/36) of Proteome Analyses. In: Becher, D. (eds) Microbial Proteomics. Methods in Molecular Biology, vol 1841. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8695-8_12
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DOI: https://doi.org/10.1007/978-1-4939-8695-8_12
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