Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP)

Analytical and Bioanalytical Chemistry

Volumn 405, Issue 12, 2013, Pages 3989-3996

  Taubert, Martin ^a,b   Von Bergen, Martin ^a,c   Seifert, Jana ^a,d  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^c AALBORG UNIVERSITY   (Denmark)

^d UNIVERSITY OF HOHENHEIM   (Germany)

Author keywords

Mass spectrometry; Protein SIP; Relative isotope abundance; Stable isotope probing

Indexed keywords

CARBON; ECOLOGY; ELECTROPHORESIS; MASS SPECTROMETRY; MICROORGANISMS; NITROGEN; PEPTIDES; PROTEOMICS;

ISOTOPE ABUNDANCE; METABOLIC ACTIVITY; MICROBIAL ACTIVITIES; MICROBIAL COMMUNITIES; ONE DIMENSIONAL GEL ELECTROPHORESIS; PSEUDOMONAS FLUORESCENS; QUANTITATIVE INVESTIGATION; STABLE-ISOTOPE PROBING;

ISOTOPES;

PSEUDOMONAS FLUORESCENS;

BACTERIAL PROTEIN; NITROGEN; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; ISOTOPE LABELING; METHODOLOGY; MOLECULAR GENETICS; PSEUDOMONAS FLUORESCENS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; ISOTOPE LABELING; MOLECULAR SEQUENCE DATA; NITROGEN ISOTOPES; PEPTIDES; PSEUDOMONAS FLUORESCENS; TANDEM MASS SPECTROMETRY;

EID: 84886088525     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-013-6828-y     Document Type: Article

References (29)

1. Dumont MG, Murrell JC (2005) Stable isotope probing-linking microbial identity to function. Nat Rev Microbiol 3(6):499-504
2. Neufeld JD, Dumont MG, Vohra J, Murrell JC (2007) Methodological considerations for the use of stable isotope probing in microbial ecology. Microbiol Ecol 53(3):435-442
3. Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68(11):5367-5373
4. Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, Murrell JC (2007) DNA stable-isotope probing. Nat Protoc 2(4):860-866
5. Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by C-13-labelling of biomarkers. Nature 392(6678):801-805
6. Jehmlich N, Schmidt F, Taubert M, Seifert J, Bastida F, von Bergen M, Richnow HH, Vogt C (2010) Protein stable isotope probing (protein-SIP). Nat Protoc 5(12):1957-1966
7. Haange SB, Oberbach A, Schlichting N, Hugenholtz F, Smidt H, von Bergen M, Till H, Seifert J (2012) Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localization resolved species distribution and enzymatic functionalities. J Proteome Res 11(11):5406-5417
8. Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, Buscot F, Richnow HH, von Bergen M, Seifert J (2012) Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J 6(12):2291-2301
9. Jehmlich N, Schmidt F, von Bergen M, Richnow HH, Vogt C (2008) Protein-based stable isotope probing (protein-SIP) reveals active species within anoxic mixed cultures. ISME J 2(11):1122-1133
10. Kermer R, Hedrich S, Taubert M, Baumann S, Schlömann M, Johnson DB, von Bergen M, Seifert J (2012) Elucidation of carbon transfer in a mixed culture of Acidiphilium cryptum and Acidithiobacillus ferrooxidans using protein-based stable isotope probing. JIOMICS 2(1):37-45
11. Morris BEL, Herbst FA, Bastida F, Seifert J, von Bergen M, Richnow HH, Suflita JM (2012) Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium. Environ Microbiol Rep 4(3):297-306
12. Seifert J, Taubert M, Jehmlich N, Schmidt F, Völker U, Vogt C, Richnow HH, Von Bergen M (2012) Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom Rev. doi:10.1002/mas.21346
13. Taubert M, Jehmlich N, Vogt C, Richnow HH, Schmidt F, von Bergen M, Seifert J (2011) Time resolved protein-based stable isotope probing (protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments. Proteomics 11(11):2265-2274
14. Taubert M, Baumann S, von Bergen M, Seifert J (2011) Exploring the limits of robust detection of incorporation of (13)C by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal Bioanal Chem 401(6):1975-1982
15. Taubert M, Vogt C, Wubet T, Kleinsteuber S, Tarkka MT, Harms H, Buscot F, Richnow HH, Von Bergen M, Seifert J (2012) Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium. ISME J. doi:10.1038/ismej.2012.68
16. van Niftrik L, Jetten MS (2012) Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties. Microbiol Mol Biol Rev 76(3):585-596
17. Ollivier J, Towe S, Bannert A, Hai B, Kastl EM, Meyer A, Su MX, Kleineidam K, Schloter M (2011) Nitrogen turnover in soil and global change. FEMS Microbiol Ecol 78(1):3-16
18. 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
19. De Biévre P, Taylor PDP (1993) Table of isotopic compositions of the elements. Int J Mass Spectrom 123(2):149-166
20. Bastida F, Rosell M, Franchini AG, Seifert J, Finsterbusch S, Jehmlich N, Jechalke S, von Bergen M, Richnow HH (2010) Elucidating MTBE degradation in a mixed consortium using a multidisciplinary approach. FEMS Microbiol Ecol 73(2):370-384
21. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567
22. Vizcaino JA, Cote R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L (2010) The proteomics identifications database: 2010 update. Nucleic Acids Res 38: D736-D742, Database issue
23. MacCoss MJ, Wu CC, Matthews DE, Yates JR (2005) Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal Chem 77(23):7646-7653
24. Whitelegge JP, Katz JE, Pihakari KA, Hale R, Aguilera R, Gomez SM, Faull KF, Vavilin D, Vermaas W (2004) Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics. Phytochemistry 65(11):1507-1515
25. Coplen TB, Bohlke JK, De Bievre P, Ding T, Holden NE, Hopple JA, Krouse HR, Lamberty A, Peiser HS, Revesz K, Rieder SE, Rosman KJR, Roth E, Taylor PDP, Vocke RD, Xiao YK (2002) Isotope-abundance variations of selected elements (IUPAC technical report). Pure Appl Chem 74(10):1987-2017
26. Elsner M (2010) Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations. J Environ Monit 12(11):2005-2031
27. Senko MW, Beu SC, Mclafferty FW (1995) Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J Am Soc Mass Spectrom 6(4):229-233
28. Kaur P, O'Connor PB (2007) Quantitative determination of isotope ratios from experimental isotopic distributions. Anal Chem 79(3):1198-1204
29. Xu Y, Heilier JF, Madalinski G, Genin E, Ezan E, Tabet JC, Junot C (2010) Evaluation of accurate mass and relative isotopic abundance measurements in the LTQ-orbitrap mass spectrometer for further metabolomics database building. Anal Chem 82(13):5490-5501