Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms

Applied Microbiology and Biotechnology

Volumn 90, Issue 2, 2011, Pages 407-416

  Porteus, Bianca ^a   Kocharunchitt, Chawalit ^a   Nilsson, Rolf E ^a   Ross, Tom ^a   Bowman, John P ^a  

^a UNIVERSITY OF TASMANIA   (Australia)

Author keywords

LTQ orbitrap; MudPIT; Protein quantification; Proteomics; Quantification; Spectral counting

Indexed keywords

MUDPIT; ORBITRAP; PROTEIN QUANTIFICATION; PROTEOMICS; QUANTIFICATION; SPECTRAL COUNTING;

GENES; METABOLISM; MICROORGANISMS; PHYSIOLOGY; PROTEINS;

MOLECULAR BIOLOGY;

PROTEOME;

COMPARATIVE STUDY; DATABASE; GEL; HYPOTHESIS TESTING; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PHYSIOLOGY; PROTEIN; PROTEOMICS; QUANTITATIVE ANALYSIS; SPECTRAL ANALYSIS;

CORYNEBACTERIUM GLUTAMICUM; GEL; GENOME; HYDROPHOBICITY; MICROORGANISM; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; PROTEOMICS; REVIEW;

BACTERIAL PROTEINS; DATABASES, PROTEIN; GELS; GENOME, BACTERIAL; LISTERIA MONOCYTOGENES; PROTEOME; PROTEOMICS; SYSTEMS BIOLOGY;

EID: 79954794882     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-011-3172-z     Document Type: Review

References (63)

1. F Al-Shahrour J Carbonell P Minguez S Goetz A Conesa J Tárraga I Medina E Alloza D Montaner J Dopazo 2010 Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments Nucleic Acids Res 36 W341 W346 10.1093/nar/gkn318
2. SM Andrew JA Titus L Zumstein 2001 Dialysis and concentration of protein solutions Curr Prot Immun 10.1002/0471142735.ima03hs21 Appendix 3H
3. C Ansong SO Purvibe JN Adkins MS Lipton RD Smith 2010 Proteogenomics: needs and roles to be filled by proteomics in genome annotation Brief Funct Genom 7 50 62 10.1093/bfgp/eln010 (Pubitemid 351721150)
4. D Becher K Hempel S Sievers D Zühlke J Pané-Farré A Otto S Fuchs D Albrecht J Bernhardt S Engelmann U Völker JM van Dijl M Hecker 2009 A proteomic view of an important human pathogen-towards the quantification of the entire Staphylococcus aureus proteome PLoS ONE 4 e8176 10.1371/journal.pone.0008176
5. Y Benjamini Y Hochberg 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing J R Statist Soc B 57 289 300
6. A Boorsma BC Foat D Vis F Klis HJ Bussemaker 2005 T-profiler: scoring the activity of predefined groups of genes using gene expression data Nucleic Acids Res 33 W592 W595 10.1093/nar/gki484 1:CAS:528:DC%2BD2MXlslyqtbk%3D (Pubitemid 44529991)
7. CA Broberg DD Clark 2010 Shotgun proteomics of Xanthobacter autotrophicus Py2 reveals proteins specific to growth on propylene Arch Microbiol 192 945 957 10.1007/s00203-010-0623-3 1:CAS:528:DC%2BC3cXht12qtb7P
8. FR Cerqueira A Graber B Schwikowski C Baumgartner 2010 MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification J Proteome Res 9 2265 2277 10.1021/pr901023v 1:CAS:528:DC%2BC3cXktlersbY%3D
9. H Choi D Fermin AI Nesvizhskii 2008 Significance analysis of spectral count data in label-free shotgun proteomics Mol Cell Prot 7 2373 2385 10.1074/mcp.M800203-MCP200 1:CAS:528:DC%2BD1cXhsFahtrzM
10. JA Christie-Oleza J Armengaud 2010 In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the Ruegeria pomeroyi DSS-3 case-study Mar Drugs 8 2223 2239 10.3390/md8082223 1:CAS:528:DC%2BC3cXpvVCrt7s%3D
11. 15N-metabolic labeling Anal Chem 73 2132 2139 10.1021/ac001487x 1:CAS:528:DC%2BD3MXhslSrsbk%3D (Pubitemid 32862424)
12. B Cooper JA Feng WM Garrett 2010 Relative, label-free protein quantitation: spectral counting error statistics from nine replicate MudPIT samples J Am Soc Mass Spectrom 21 1534 1546 10.1016/j.jasms.2010.05.001 1:CAS:528:DC%2BC3cXhtVKiurrM
13. CL de Hoog M Mann 2004 Proteomics Annu Rev Genomics Hum Genet 5 267 293 10.1146/annurev.genom.4.070802.110305 (Pubitemid 39362748)
14. JA Dowell DC Frost J Zhang L Li 2008 Comparison of two-dimensional fractionation techniques for shotgun proteomics Anal Chem 80 6715 6723 10.1021/ac8007994 1:CAS:528:DC%2BD1cXpt1yns7c%3D
15. A Eshgi PA Cullen L Cowen RL Zuerner CE Cameron 2009 Global proteome analysis of Leptospira interrogans J Prot Res 8 4564 4578 10.1021/pr9004597
16. AM Feist B∅ Palsson 2008 The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli Nat Biotechnol 26 659 667 10.1038/nbt1401 1:CAS:528:DC%2BD1cXmvVCju7Y%3D (Pubitemid 351824691)
17. F Fischer A Poetsch 2006 Protein cleavage strategies for an improved analysis of the membrane proteome Proteome Sci 4 2 10.1186/1477-5956-4-2
18. F Forner LJ Foster S Campanaro G Valle M Mann 2006 Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver Mol Cell Proteomics 5 144 156
19. B Fränzel F Fischer C Trötschel A Poetsch D Wolters 2009 The two-phase partitioning system-a powerful technique to purify integral membrane proteins of Corynebacterium glutamicum for quantitative shotgun analysis Proteomics 9 2263 2272 10.1002/pmic.200800766
20. B Fränzel A Poetsch C Trötschel M Persicke J Kalinoswski DA Wolters D Andreas 2010 Quantitative proteomic overview on the Corynebacterium glutamicum L-lysine producing strain DM1730 J Proteomics 73 2336 2353 10.1016/j.jprot.2010.07.006
21. X Fu SA Gharib PS Gren ML Aitken DA Frazer DR Park T Vaisar JW Heinecke 2008 Spectral index for assessment of differential protein expression in shotgun proteomics J Proteome Res 7 845 854 10.1021/pr070271+ 1:CAS:528: DC%2BD1cXntlKnsA%3D%3D
22. SA Gerber J Rush O Stemman MW Kirschner SP Gygi 2003 Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proc Natl Acad Sci USA 100 6940 6945 10.1073/pnas.0832254100 1:CAS:528:DC%2BD3sXkslOnt7Y%3D (Pubitemid 36706372)
23. NM Griffin J Yu F Long P Oh S Shore Y Li JA Koziol JE Schnitzer 2009 Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis Nat Biotechnol 28 83 89 10.1038/nbt.1592
24. SP Gygi B Rist SA Gerber F Turecek MH Gelb R Aebersold 1999 Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat Biotechnol 17 994 999 10.1038/13690 1:CAS:528:DyaK1MXmvVelsLs%3D (Pubitemid 29474856)
25. H Hahne S Wolff M Hecker D Becher 2008 From complementarity to comprehensiveness-targeting the membrane proteome of growing Bacillus subtilis by divergent approaches Proteomics 8 4123 4136 10.1002/pmic.200800258 1:CAS:528:DC%2BD1cXht1Kgur7K
26. M Hecker S Engelmann SJ Cordwell 2003 Proteomics of Staphylococcus aureus-current state and future challenges J Chromatogr 787 179 195 10.1016/S1570-0232(02)00907-8 1:CAS:528:DC%2BD3sXjtFSmsrs%3D (Pubitemid 36351273)
27. EL Hendrickson DAC Beck TS Wang ME Lidstrom M Hackett L Chistoserdova 2010 Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy J Bacteriol 192 4859 4867 10.1128/JB.00512-10 1:CAS:528:DC%2BC3cXhsFCitbzE
28. Q Hu RJ Noll H Li A Makarov M Hardman R Graham Cooks 2005 The Orbitrap: a new mass spectrometer J Mass Spectrom 40 430 443 10.1002/jms.856 1:CAS:528:DC%2BD2MXktFKjtbw%3D (Pubitemid 40637866)
29. Y Ishihama Y Oda T Tabata T Sato T Nagasu J Rappsilber M Mann 2005 Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein Mol Cell Proteomics 4 1265 1272 10.1074/mcp.M500061-MCP200 1:CAS:528:DC%2BD2MXhtVGhu7nL (Pubitemid 41448714)
30. Y Ishihama T Schmidt J Rappsilber M Mann F Ulrich Hartl MJ Kerner D Frishman 2008 Protein abundance profiling of the Escherichia coli cytosol BMC Genomics 9 102 10.1186/1471-2164-9-102 (Pubitemid 351517450)
31. RE Jabbour SV Deshpande MM Wade MF Stanford CH Wick AW Zulich EW Skowronski AP Snyder 2010 Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics Appl Environ Microbiol 76 3637 3644 10.1128/AEM.00055-10 1:CAS:528:DC%2BC3cXot1Cgu7g%3D
32. M Kanehisa S Goto S SK A Nakaya 2002 The KEGG databases at GenomeNet Nucleic Acids Res 30 42 46 10.1093/nar/30.1.42 1:CAS:528:DC%2BD38Xht12ksbc%3D
33. D Karp CA Ouzounis C Moore-Kochlacs L Goldovsky P Kaipa D Ahren S Tsoka N Darzentas V Kunin N Lopez-Bigas 2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Nucleic Acids Res 19 6083 6089 10.1093/nar/gki892 (Pubitemid 41742547)
34. IM Keseler C Bonavides-Martinez J Collado-Vides S Gama-Castro RP Gunsalus DA Johnson M Krummenacker LM Nolan S Paley IT Paulsen M Peralta-Gil A Santos-Zavaleta AG Shearer PD Karp 2009 EcoCyc: a comprehensive view of Escherichia coli biology Nucleic Acids Res 37 D464 D470 10.1093/nar/gkn751 1:CAS:528:DC%2BD1cXhsFejtLvO
35. JM Lee EP Gianchandani JA Papin 2006 Flux balance analysis in the era of metabolomics Brief Bioinform 7 140 150 10.1093/bib/bbl007 (Pubitemid 44404880)
36. S Luche V Santoni T Rabilloud 2003 Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis Proteomics 3 249 253 10.1002/pmic.200390037 1:CAS:528: DC%2BD3sXisVCgu7w%3D (Pubitemid 36343680)
37. DH Lundgren SI Hwang L Wu DK Han 2010 Role of spectral counting in quantitative proteomics Expert Rev Proteomics 7 39 53 10.1586/epr.09.69 1:CAS:528:DC%2BC3cXhtlOitbs%3D
38. OA Mirgorodskaya YP Kozmin MI Titov R Korner CP Sonksen P Roepstorff 2000 Quantification of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using (18) O-labeled internal standards Rapid Commun Mass Spectrom 14 1226 1232 10.1002/1097-0231(20000730)14: 14<1226::AID-RCM14>3.0.CO;2-V 1:CAS:528:DC%2BD3cXltlyls7g%3D (Pubitemid 30489495)
39. G Mitulović K Mechtler 2006 HPLC techniques for proteomics analysis-a short overview of latest developments Brief Funct Genomic Proteomic 5 249 260 10.1093/bfgp/ell034 (Pubitemid 46404129)
40. DA Natale CN Arighi WC Barker J Blake TC Chang Z Hu H Liu B Smith CH Wu 2007 Framework for a protein ontology BMC Bioinform 8 Suppl 9 S1 10.1186/1471-2105-8-S9-S1
41. AI Nesvizhskii A Keller E Kolker R Aebersold 2003 A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 75 4646 4658 10.1021/ac0341261 1:CAS:528:DC%2BD3sXltlynt70%3D (Pubitemid 37082259)
42. AI Nesvizhskii O Vitek R Aebersold 2007 Analysis and validation of proteomic data generated by tandem mass spectrometry Nat Meth 4 787 797 10.1038/nmeth1088 1:CAS:528:DC%2BD2sXhtV2mtr%2FK (Pubitemid 350055575)
43. J Noirel SY Ow G Sanguintti PC Wright 2009 Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring Mol Biosyst 5 1214 1223 10.1039/b904729h 1:CAS:528:DC%2BD1MXhtFarsb7P
44. WM Old K Meyer-Arendt L Aveline-Wolf KG Pierce A Mendoza JR Sevinsky KA Resing NG Ahn 2005 Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol Cell Proteomics 4 1487 1502 10.1074/mcp.M500084-MCP200 1:CAS:528:DC%2BD2MXhtFeltbzI (Pubitemid 41555475)
45. SE Ong B Blagoev I Kratchmarova DB Kristensen H Steen A Pandey M Mann 2002 Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol Cell Proteomics 1 376 386 10.1074/mcp.M200025-MCP200 1:CAS:528:DC%2BD38XlslWhsrk%3D
46. S Orchard A Jones JP Albar SY Cho KH Kwon C Lee H Hermjakob 2010 Tackling quantitation: a report on the annual spring workshop of the HUPO-PSI Proteomics 10 3062 3066 10.1002/pmic.201090075 1:CAS:528:DC%2BC3cXhtV2gsb3K
47. JD Orth I Thiele B∅ Palsson 2010 What is flux balance analysis? Nat Biotechnol 28 245 248 10.1038/nbt.1614 1:CAS:528:DC%2BC3cXivV2rtL4%3D
48. A Otto J Bernhardt H Meyer M Schaffer FA Herst J Siebourg U Mäder M Lalk M Hecker D Becher 2010 Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis Nature Comm 1 9 137 10.1038/ncomms1137
49. TV Pham SR Piersma M Warmoes CR Jimenez 2010 On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics Bioinformatics 26 363 369 10.1093/bioinformatics/btp677 1:CAS:528:DC%2BC3cXhs1Onsr4%3D
50. JM Prattl DM Simpson MK Doherty J Rivers SJ Gaskell RJ Beynon 2006 Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes Nat Protocol 1 1029 1043 10.1038/nprot.2006. 129
51. J Rappsilber U Ryder AI Lamond M Mann 2002 Large-scale proteomic analysis of the human spliceosome Genome Res 12 1231 1245 10.1101/gr.473902 1:CAS:528:DC%2BD38Xmtl2rur4%3D (Pubitemid 41264425)
52. B Rietschel TN Arrey B Meyer S Bornemann M Schuerken M Karas A Poetsch 2009 Elastase digests: new ammunition for shotgun membrane proteomics Mol Cell Proteomics 8 1029 1043 10.1074/mcp.M800223-MCP200 1:CAS:528:DC%2BD1MXmtlGqtb8%3D
53. PL Ross YLN Huang JN Marchese B Williamson K Parker S Hattan N Khainovski S Pillai S Dey S Daniels S Purkayastha P Juhasz S Martin M Bartlet-Jones F He A Jacobson DJ Pappin 2004 Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol Cell Proteomics 3 1154 1169 10.1074/mcp.M400129-MCP200 1:CAS:528:DC%2BD2MXhvFartg%3D%3D
54. SL Sanders J Jennings A Canutescu AJ Link PA Weil 2002 Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry Mol Cell Biol 22 4723 4738 10.1128/MCB.22.13.4723-4738.2002 1:CAS:528:DC%2BD38Xks1yrtr8%3D (Pubitemid 34620408)
55. IP Shadforth PJ Dunnley KS Lilley C Bessant 2005 i-Tracker: for quantitative proteomics using iTRAQ BMC Genomics 6 145 10.1186/1471-2164-6-145 (Pubitemid 41631205)
56. KEJ Tyo K Kocharin J Nielsen 2010 Toward design-based engineering of industrial microbes Curr Opin Microbiol 13 255 262 10.1016/j.mib.2010.02.001 1:CAS:528:DC%2BC3cXntVSlurw%3D
57. DA Williams 1976 Improved likelihood ratio test for complete contingency tables Biometrika 63 33 37 10.1093/biomet/63.1.33
58. P Wilmes PL Bond 2006 Metaproteomics: studying functional gene expression in microbial ecosystems Trends Microbiol 14 92 97 10.1016/j.tim.2005.12.006 1:CAS:528:DC%2BD28XhtlGjt7o%3D (Pubitemid 43190739)
59. P Wilmes BP Bowen BC Thomas RS Mueller VJ Denef NC VerBerkmoes RL Hettich TR Northen JF Banfield 2010 Metabolome-proteome differentiation coupled to microbial divergence MBio 1 5 e00246-10 10.1128/mBio.00246-10
60. JR Yates CI Ruse A Nakorchevsky 2009 Proteomics by mass spectrometry: approaches, advances, and applications Annu Rev Biomed Eng 11 49 79 10.1146/annurev-bioeng-061008-124934 1:CAS:528:DC%2BD1MXhtVKmt7fP
61. K Yizhak T Benyamini W Liebermeister E Ruppin T Shlomi 2010 Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model Bioinformatics 26 255 260 10.1093/bioinformatics/btq183
62. B Zhang NC VerBerkmoes MA Langston E Uberbacher RL Hettich NF Samatova 2006 Detecting differential and correlated protein expression in label-free shotgun proteomics J Proteome Res 5 2909 2918 10.1021/pr0600273 1:CAS:528:DC%2BD28XhtVGmsbvI (Pubitemid 44749209)
63. B Zybailov AL Mosley ME Sardiu MK Coleman L Florens MP Washburn 2006 Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae J Proteome Res 5 2339 2347 10.1021/pr060161n 1:CAS:528: DC%2BD28XnsV2gs7g%3D (Pubitemid 44330827)