Label-Free detection of differential protein expression by LC/MALDI mass spectrometry

Journal of Proteome Research

Volumn 7, Issue 6, 2008, Pages 2270-2279

  Neubert, Hendrik ^a   Bonnert, Timothy P ^b   Rumpel, Klaus ^a   Hunt, Brandon T ^b   Henle, Ernst S ^b   Lames, Ian T ^a  

^a PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^b Hoddesdon   (United Kingdom)

Author keywords

E.Coli; Label free; LC MALDI; Protein expression; Proteomics

Indexed keywords

ARABINOSE; CARBON; FRUCTOSE; GLUCOSE; ESCHERICHIA COLI PROTEIN; PROTEIN; PROTEOME; TRYPSIN;

ARTICLE; ESCHERICHIA COLI; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; DRUG EFFECT; GROWTH, DEVELOPMENT AND AGING; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INFORMATION PROCESSING; METABOLISM; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY;

ESCHERICHIA COLI;

ARABINOSE; AUTOMATIC DATA PROCESSING; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FRUCTOSE; GLUCOSE; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 49849105549     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr700705u     Document Type: Article

References (52)

1. Ong, S.-E.; Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
2. Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell. Biol. 2006, 7, 952-958.
3. Julka, S.; Regnier, F. Quantification in proteomics through stable isotope coding: A review. J. Proteome Res. 2004, 3, 350-363.
4. Leitner, A.; Lindner, W. Chemistry meets proteomics: The use of chemical tagging reactions for MS-based proteomics. Proteomics 2006, 6, 5418-5434.
5. Colinge, J.; Chiappe, D.; Lagache, S.; Moniatte, M.; Bougueleret, L. Differential proteomics via probabilistic peptide identification scores. Anal. Chem. 2005, 77, 596-606.
6. Gaspari, M.; Verhoeckx, K. C. M.; Verheij, E. R.; vanderGreef, J. Integration of two-dimensional LC-MS with multivariate statistics for comparative analysis of proteomic samples. Anal. Chem. 2006, 78, 2286-2296.
7. Meng, F.; et al. Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry. J. Am. Soc. Mass Spectrom. 2007, 18, 226-233.
8. Old, W. M. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
9. Prakash, A. Signal maps for mass spectrometry-based comparative proteomics. Mol. Cell. Proteomics 2006, 5, 423-432.
10. Silva, J. C. Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
11. Stewart, I. I. The reproducible acquisition of comparative liquid chromatography/tandem mass spectrometry data from complex biological samples. Rapid Commun. Mass Spectrom. 2004, 18, 1697-1710.
12. Wang, W. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 2003, 75, 4818-826.
13. Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates, N. A. Differential mass spectrometry: A label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal. Chem. 2004, 76, 6085-6096.
14. Higgs, R. E.; Knierman, M. D.; Gelfanova, V.; Butler, J. P.; Hale, J. E. Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res. 2005, 4, 1442-1450.
15. Chelius, D.; Bondarenko, P. V. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res. 2002, 1, 317-323.
16. Wang, G.; Wu, W. W.; Zeng, W.; Chou, C. L.; Shen, R. F. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J. Proteome Res. 2006, 5, 1214-1223.
17. Gillette, M. A.; Mani, D. R.; Carr, S. A. Place of pattern in proteomic biomarker discovery. J. Proteome Res. 2005, 4, 1143-1154.
18. Roy, S. M.; Anderle, M.; Lin, H.; Becker, C. H. Differential expression profiling of serum proteins and metabolites for biomarker discovery. Int. J. Mass Spectrom. 2004, 238, 163-171.
19. Follettie, M. T. Organ messenger ribonucleic acid and plasma proteome changes in the adjuvant-induced arthritis model: Responses to disease induction and therapy with the estrogen receptor-(beta} selective agonist ERB-041. Endocrinology 2006, 147, 714-723.
20. Kantor, A. B. Biomarker discovery by comprehensive phenotyping for autoimmune diseases. Clin. Immunol. 2004, 111, 186-195.
21. Chan, E. Y. Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production. J. Virol. 2007, 81, 7571-7583.
22. Liu, H.; Sadygov, R. G.; Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
23. Ghaemmaghami, S. Global analysis of protein expression in yeast. Nature 2003, 425, 737-741.
24. Gao, J.; Friedrichs, M. S.; Dongre, A. R.; Opiteck, G. J. Guidelines for the routine application of the peptide hits technique. J. Am. Soc. Mass Spectrom. 2005, 16, 1231-1238.
25. Ishihama, Y. 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 2005, 4, 1265-1272.
26. Rappsilber, J.; Ryder, U.; Lamond, A. I.; Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12, 1231-1245.
27. Lu, P.; Vogel, C; Wang, R.; Yao, X.; Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25, 117-124.
28. Randolph, T. W.; Mitchell, B. L.; McLerran, D. F.; Lampe, P. D.; Feng, Z. Quantifying peptide signal in MALD1-TOF mass spectrometry data. Mol. Cell. Proteomics 2005, 4, 1990-1999.
29. Beynon, R. J.; Doherty, M. K.; Pratt, J. M.; Gaskell, S. J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2005, 2, 587-589.
30. Wei, H. Identification and quantification of neuropeptides in brain tissue by capillary liquid chromatography coupled off-line to MALDI-TOF and MALDI-TOF/TOF-MS. Anal. Chem. 2006, 78, 4342-4351.
31. Wa, C; Cerny, R. L.; Hage, D. S. Identification and quantitative studies of protein immobilization sites by stable isotope labeling and mass spectrometry. Anal. Chem. 2006, 78, 7967-7977.
32. Villanueva, J.; et al. Serum peptide profiling by magnetic particle- assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 2004, 76, 1560-1570.
33. Hattan, S. J.; Marchese, J.; Khainovski, N.; Martin, S.; Juhasz, P. Comparative study of [three] LC-MALDI workflows for the analysis of complex proteomic samples. J. Proteome Res. 2005, 4, 1931- 1941.
34. Ji, C. J.; Li, L. Quantitative proteome analysis using differential stable isotopic labeling and microbore LC-MALDI MS and MS/MS. J Proteome Res. 2005, 4, 734-742.
35. Mirgorodskaya, E.; Braeue, C; Fucini, P.; Lehrach, H.; Gobom, L. Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: Sample preparation, data analysis, and application to the analysis of complex peptide mixtures. Proteomics 2005, 5, 399-408.
36. Zhen, Y. Development of an LC-MALDI method for the analysis of protein complexes. J. Am. Soc. Mass Spectrom. 2004, 15, 803- 822.
37. Bodnar, W. M.; Blackburn, R. K.; Krise, J. M.; Moseley, M. A. Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. J Am. Soc. Mass Spectrom. 2003, 14, 971-979.
38. Chen, H. S.; Rejtar, T.; Andreev, V.; Moskovets, E.; Karger, B. L. Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: Exclusion of redundant peptides from MS/ MS analysis in replicate runs. Anal. Chem. 2005, 77, 7816-7825.
39. Chen, H. S.; Rejtar, T.; Andreev, V.; Moskovets, E.; Karger, B. L. High-speed, high-resolution monolithic capillary LC-MALDI MS using an off-line continuous deposition interface for proteomic analysis. Anal. Chem. 2005, 77, 2323-2331.
40. Roesli, C; Elia, G.; Neri, D. Two-dimensional mass spectrometric mapping. Curr. Opin. Chem. Biol. 2006, 10, 35-41.
41. Tammen, H.; et al. Peptidomic analysis of human blood specimens: Comparison between plasma specimens and serum by differential peptide display. Proteomics 2005, 5, 3414-3422.
42. Hattan, S. L; Parker, K. C. Methodology utilizing MS signal intensity and LC retention time for quantitative analysis and precursor ion selection in proteomic LC-MALDI analyses. Anal. Chem. 2006, 78, 7986-7996.
43. Garden, R. W.; Sweedler, J. V. Heterogeneity within MALDI samples as revealed by mass spectrometric imaging. Anal. Chem. 2000, 72, 30-36.
44. Palagi, P. M.; Hernandez, P.; Walther, D.; Appel, R. D. Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics 2006, 6, 5435-5444.
45. Li, X. J. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal. Chem. 2004, 76, 3856-3860.
46. Johansson, C. Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC- MS/MS data. Proteomics 2006, 6, 4475-485.
47. Palagi, P. M. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005, 5, 2381- 2384.
48. Leptos, K. C; Sarracino, D. A.; Jaffe, J. D.; Krastins, B.; Church, G. M. MapQuant: Open-source software for large-scale protein quantification. Proteomics 2006, 6, 1770-1782.
49. Berg, M.; Parbel, A.; Pettersen, H.; Fenyo, D.; Bjorkesten, L. Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization. Rapid Commun. Mass Spectrom. 2006, 20, 1558-1562.
50. Mayr, B. M. Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res. 2006, 5, 414-421.
51. Schleif, R. Regulation of the -arabinose operon of Escherichia coli. Trends Genet. 2000, 16, 559-565.
52. Xu, Y. Chaperone-mediated folding and maturation of the penicillin acylase precursor in the cytoplasm of Escherichia coli. Appl. Environ. Microbiol. 2005, 71, 6247-6253.