Comparison of a Salmonella typhimurium proteome defined by shotgun proteomics directly on an LTQ-FT and by proteome pre-fractionation on an LCQ-DUO

Briefings in Functional Genomics and Proteomics

Volumn 5, Issue 2, 2006, Pages 154-168

  Nunn, Brook L ^b   Shaffer, Scott A ^b   Scherl, Alexander ^b   Gallis, Byron ^b   Wu, Manhong ^b   Miller, Samuel I ^b   Goodlett, David R ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b NONE

Author keywords

Ion trap mass spectrometer; Linear ion trap and Fourier transform ion cyclotron resonance mass spectrometer; Membrane proteome; Salmonella; Shotgun proteomics

Indexed keywords

BACTERIAL PROTEIN; MEMBRANE PROTEIN; PHOP PROTEIN; PROTEOME; TRYPSIN;

ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; CONTROLLED STUDY; INTERMETHOD COMPARISON; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; ION TRAP MASS SPECTROMETRY; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MASS SPECTROMETRY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEOMICS; SALMONELLA TYPHIMURIUM; TANDEM MASS SPECTROMETRY; CHEMISTRY; COMPARATIVE STUDY; FOURIER ANALYSIS; GENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; METABOLISM; METHODOLOGY; MUTATION; REVIEW;

SALMONELLA; SALMONELLA TYPHIMURIUM;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; FOURIER ANALYSIS; MASS SPECTROMETRY; MUTATION; PROTEOME; PROTEOMICS; SALMONELLA TYPHIMURIUM; TRYPSIN;

EID: 33748539720     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/ell024     Document Type: Article

References (34)

1. Yao X, Freas A, Ramirez J, et al. Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus. Anal Chem 2001;73:2836-42.
2. McDonald WH, Yates JR 3rd. Shotgun proteomics: Integrating technologies to answer biological questions. Curr Opin Mol Ther 2003;5:302-9.
3. Chen EI, Hewel J, Felding-Habermann B, John R, Yates I. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT). Mol Cell Proteomics 2006;5:53-6.
4. Wu SL, Choudhary G, Ramstrom M, et al. Evaluation of shotgun sequencing for proteomic analysis of human plasma using HPLC coupled with either ion trap or Fourier transform mass spectrometry. J Proteome Res 2003; 2:383-93.
5. Florens L, Liu X, Wang Y, et al. Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes. Mol Biochem Parasitol 2004;135:1-11.
6. Radulovic D, Jelveh S, Ryu S, et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 2004;3:984-97.
7. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 2004;4:59-77.
8. Lu H, Li W, Noble WS, et al. Riboproteomics of the hepatitis C virus internal ribosomal entry site. J Proteome Res 2004;3:949-57.
9. McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery. Dis Markers 2002;18:99-105.
10. Tsur D, Tanner S, Zandi E, et al. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol 2005;23:1562-7.
11. Syka JE, Marto JA, Bai DL, et al. Novel linear quadrupole ion trap/FT mass spectrometer: Performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J Proteome Res 2004;3:621-6.
12. Gunn JS, Ernst RK, McCoy AJ, Miller SI. Constitutive mutations of the salmonella enterica serovar typhimurium transcriptional virulence regulator phoP. Infect and Immun 2000;68:3758-62.
13. Zhang H, Yi EC, Li X, et al. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics 2005;4:144-55.
14. Link AJ, Eng J, Schieltz DM, et al. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 1999;17: 676.
15. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002;74:5383-92.
16. Yi EC, Marelli M, Lee H, et al. Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis 2002;23:3205-16.
17. Spahr CS, Davis MT, McGinley MD, et al. Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. I. Profiling an unfractionated tryptic digest. Proteomics 2001;1:93-107.
18. Washburn MP, Wolters D, JRY, III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19:242.
19. Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-38.
20. Stevens TJ, Arkin IT. Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins 2000;39:417-20.
21. Wu CC, Yates JR 3rd. The application of mass spectrometry to membrane proteomics. Nat Biotechnol 2003;21: 262-7.
22. Molloy MP, Herbert BR, Walsh BJ, et al. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 1998;19:837-44.
23. Rabilloud T. Use of thiourea to increase the solubility of membrane proteins in two-dimensional electrophoresis. Electrophoresis 1998;19:758-60.
24. Luche S, Santoni V, Rabilloud T. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis. Proteomics 2003;3: 249-53.
25. Deshusses JM, Burgess JA, Scherl A, et al. Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins. Proteomics 2003;3: 1418-24.
26. Zuo X, Speicher DW. Comprehensive analysis of complex proteomes using microscale solution isoelectrofocusing prior to narrow pH range two-dimensional electrophoresis. Proteomics 2002;2:58-68.
27. Adessi C, Miege C, Albrieux C, Rabilloud T. Two-dimensional electrophoresis of membrane proteins: A current challenge for immobilized pH gradients. Electrophoresis 1997;18:127-35.
28. Chevallet M, Santoni V, Poinas A, et al. New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 1998;19: 1901-9.
29. Galvani M, Rovatti L, Hamdan M, et al. Protein alkylation in the presence/absence of thiourea in proteome analysis: A matrix assisted laser desorption/ionization-time of flight-mass spectrometry investigation. Electrophoresis 2001;22: 2066-74.
30. Schwartz R, Ting CS, King J. Whole proteome pI values correlate with subcellular localizations of proteins for organisms within the three domains of life. Genome Res 2001;11:703-9.
31. Zuo X, Hembach P, Echan L, Speicher David W. Enhanced analysis of human breast cancer proteomes using micro-scale solution isoelectrofocusing combined with high resolution 1-D and 2-D gels. J Chromatogr 2002; 782:253-65.
32. Invitrogen. Enhance your protein profile using ZOOM IEF fractionator. In: Invitrogen life technologies 2004.
33. Gardy JL, Laird MR, Chen F, et al. PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 2005;21:617-23.
34. Sillero A, Ribeiro JM. Isoelectric points of proteins: Theoretical determination. Anal Biochem 1998;179:319-25.