Which metaproteome? The impact of protein extraction bias on metaproteomic analyses

Molecular and Cellular Probes

Volumn 27, Issue 5-6, 2013, Pages 193-199

  Leary, Dagmar Hajkova ^a   Hervey, W Judson ^a   Deschamps, Jeffrey R ^a   Kusterbeck, Anne W ^a   Vora, Gary J ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

Author keywords

Biofilm; Biological mass spectrometry; Community proteomics; Environmental proteomics; LC MS MS; Metaproteomics

Indexed keywords

CITRATE PHENOL; GUANIDINE; METAPROTEOME; PHENOL DERIVATIVE; PROTEOME; UNCLASSIFIED DRUG;

ARTICLE; BIOFILM; CALCIUM BINDING; CARBOHYDRATE METABOLISM; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MEMBRANE TRANSPORT; OXIDATIVE STRESS; PHOTOSYNTHESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEOMICS; SPECIES COMPOSITION;

EUKARYOTA; PROKARYOTA;

BIOFILM; BIOLOGICAL MASS SPECTROMETRY; COMMUNITY PROTEOMICS; ENVIRONMENTAL PROTEOMICS; LC-MS/MS; METAPROTEOMICS;

BIOFILMS; CITRATES; DATABASES, PROTEIN; GUANIDINE; INDICATORS AND REAGENTS; MASS SPECTROMETRY; PHENOL; PROTEINS; PROTEOME; PROTEOMICS;

EID: 84884164276     PISSN: 08908508     EISSN: 10961194     Source Type: Journal    
DOI: 10.1016/j.mcp.2013.06.003     Document Type: Article

References (21)

1. Wilmes P., Bond P.L. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 2006, 14:92-97.
2. Schneider T., Riedel K. Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 2010, 10:785-798.
3. Lacerda C.M., Reardon K.F. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. Brief Funct Genomic Proteomic 2009, 8:75-87.
4. Abram F., Gunnigle E., O'Flaherty V. Optimisation of protein extraction and 2-DE for metaproteomics of microbial communities from anaerobic wastewater treatment biofilms. Electrophoresis 2009, 30:4149-4151.
5. Leary D.H., Hervey W.J., Li R.W., Deschamps J.R., Kusterbeck A.W., Vora G.J. Method development for metaproteomic analyses of marine biofilms. Anal Chem 2012, 84:4006-4013.
6. Chourey K., Jansson J., VerBerkmoes N., Shah M., Chavarria K.L., Tom L.M., et al. Direct cellular lysis/protein extraction protocol for soil metaproteomics. JProteome Res 2010, 9:6615-6622.
7. Pierre-Alain M., Christophe M., Severine S., Houria A., Philippe L., Lionel R. Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb Ecol 2007, 53:426-434.
8. Keiblinger K.M., Wilhartitz I.C., Schneider T., Roschitzki B., Schmid E., Eberl L., et al. Soil metaproteomics - comparative evaluation of protein extraction protocols. Soil Biol Biochem 2012, 54:14-24.
9. Chen S., Rillig M.C., Wang W. Improving soil protein extraction for metaproteome analysis and glomalin-related soil protein detection. Proteomics 2009, 9:4970-4973.
10. Maron P.A., Ranjard L., Mougel C., Lemanceau P. Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 2007, 53:486-493.
11. VerBerkmoes N.C., Denef V.J., Hettich R.L., Banfield J.F. Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 2009, 7:196-205.
12. Dowd W.W. Challenges for biological interpretation of environmental proteomics data in non-model organisms. Integr Comp Biol 2012, 52:705-720.
13. Thompson M.R., Chourey K., Froelich J.M., Erickson B.K., VerBerkmoes N.C., Hettich R.L. Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Anal Chem 2008, 80:9517-9525.
14. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. JMol Biol 2001, 305:567-580.
15. Hurkman W.J., Tanaka C.K. Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis. Plant Physiol 1986, 81:802-806.
16. Carpentier S.C., Witters E., Laukens K., Deckers P., Swennen R., Panis B. Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 2005, 5:2497-2507.
17. Yiou P., Shaoli A., Kebin L., Tao W., Kui F., Hua Z., et al. Evaluation of extraction procedures for 2-DE analysis of aphid proteins. JSep Sci 2013, 36:532-539.
18. Shi Y., Tyson G.W., Eppley J.M., DeLong E.F. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 2011, 5:999-1013.
19. Wilmes P., Wexler M., Bond P.L. Metaproteomics provides functional insight into activated sludge wastewater treatment. PloS One 2008, 3:e1778.
20. Gao L., Tao D., Shan Y., Liang Z., Zhang L., Huo Y., et al. HPLC-MS/MS shotgun proteomic research of deer antlers with multiparallel protein extraction methods. JChromatogr B Analyt Technol Biomed Life Sci 2010, 878:3370-3374.
21. Goltsman D.S., Denef V.J., Singer S.W., VerBerkmoes N.C., Lefsrud M., Mueller R.S., et al. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 2009, 75:4599-4615.