Technological advancements in mass spectrometry and its impact on proteomics

Analytical Letters

Volumn 44, Issue 8, 2011, Pages 1498-1520

  Kollipara, Sivacharan ^a   Agarwal, Nitin ^a   Varshney, Brijesh ^a   Paliwal, Jyoti ^a  

^a RANBAXY RESEARCH LABORATORIES   (India)

Author keywords

Ion fragmentation; Ionization; Mass analysis; Mass spectrometry; Proteomics

Indexed keywords

EID: 79959189042     PISSN: 00032719     EISSN: 1532236X     Source Type: Journal    
DOI: 10.1080/00032719.2010.520386     Document Type: Review

References (100)

1. Bailey, C. M., S. M. M. Sweet, D. L. Cunningham, M. Zeller, J. K. Heath, and H. J. Cooper. 2009. SLoMo: Automated site localization of modifications from ETD/ECD mass spectra. J. Proteome. Res. 8: 1965-1971.
2. Bakhtiar, R., and Z. Guan. 2006. Electron capture dissociation mass spectrometry in characterization of peptides and proteins. Biotechnol. Lett. 28: 1047-1059.
3. Bogdanov, B., and R. D. Smith. 2005. Proteomics by FTICR mass spectrometry: Top down and bottom up. Mass Spectrom. Rev. 24: 168-200.
4. Brock, A., D. M. Horn, E. C. Peters, C. M. Shaw, C. Ericson, Q. T. Phung, and A. R. Salomon. 2002. Automated liquid chromatography MALDI-FTICR-MS platform for proteomics. Automated high performance mass spectrometry and data analysis. Am. Pharm. Rev. 5: 94-99.
5. Brodbelt, J. S., and J. L. Wilson. 2009. Infrared multiphoton dissociation in quadrupole ion traps. Mass Spectrom. Rev. 28: 390-424.
6. Chamot-Rooke, J., G. van der Rest, A. Dalleu, S. Bay, and J. Lemoine. 2007. The combination of electron capture dissociation and fixed charge derivatization increases sequence coverage for O-glycosylated and O-phosphorylated peptides. J. Am. Soc. Mass Spectrom. 18: 1405-1413.
7. Chapman, K. 2002. The ProteinChip1 biomarker system from Ciphergen Biosystems: A novel proteomics platform for rapid biomarker discovery and validation. Biochem. Soc. Trans. 30: 82-87.
8. Chen, C. H. 2008. Review of a current role of mass spectrometry for proteome research. Anal Chim Acta. 624: 16-36.
9. Cole, R. B. 1997. Combining liquid chromatography with electrospray mass spectrometry. In Electrospray Ionization Mass Spectrometry: Fundamentals, Instrumentation and Applications, 1st ed., 323-342. New York: Wiley.
10. Colinge, J., A. Masselot, M. Giron, T. Dessingy, and J. Magnin. 2003. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics. 3: 1454-1463.
11. Cooper, H. J., K. Hakansson, and A. G. Marshall. 2005. The role of electron capture dissociation in biomolecular analysis. Mass Spectrom. Rev. 24: 201-222.
12. Craig, R., and R. C. Beavis. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics. 20: 1466-1467.
13. Dodds, E. D., J. B. German, and C. B. Lebrilla. 2007. Enabling MALDI-FTICR-MS=MS for high-performance proteomics through combination of infrared and collisional activation. Anal. Chem. 79: 9547-9556.
14. Drogaris, P., J. C. Le Blanc, J. E. Fitzgerald, N. F. Lowndes, A. Verreault, and P. Thibault. 2009. Enhanced protein detection using a trapping mode on a hybrid quadrupole linear ion trap (Q-Trap). Anal. Chem. 81: 6300-6309.
15. Eng, J. K., A. L. McCormack, and J. R. Yates. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5: 976-989.
16. Gardner, M. W., S. I. Smith, A. R. Ledvina, J. A. Madsen, J. J. Coon, J. C. Schwartz, G. C. Stafford, and J. S. Brodbelt. 2009. Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer. Anal. Chem. 81: 8109-8118.
17. Ge, F., and Q. Y. He. 2009. Genomic and proteomic approaches for predicting toxicity and adverse drug reactions. Expert Opin. Drug Metabol. Toxicol. 5: 29-37.
18. Geer, L. Y., S. P. Markey, J. A. Kowalak, L. Wagner, M. Xu, D. M. Maynard, X. Yang, W. Shi, and S. H. Bryant. 2004. Open mass spectrometry search algorithm. J. Proteome Res. 3: 958-964.
19. Hager, J. W. 2004. QTRAPTM mass spectrometer technology for proteomics and applications. Drug Discovery Today. 3: S31-S36.
20. Hakansson, K., M. J. Chalmers, J. P. Quinn, M. A. McFarland, C. L. Hendrickson, and A. G. Marshall. 2003. Combined electron capture and infrared multiphoton dissociation for multistage MS/MS in a Fourier transform ion cyclotron resonance mass spectrometer. Anal. Chem. 75: 3256-3262.
21. Han, X., A. Aslanian, and J. R. Yates. 2008. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 12: 483-490.
22. Hashimo, Y., H. Hasegawa, K. Yoshinari, and I. Waki. 2003. Collision-activated infrared multiphoton dissociation in a quadrupole ion trap mass spectrometer. Anal. Chem. 75: 420-425.
23. Hillenkamp, F., and J. Peter-Katalinić. 2007. MALDI mass spectrometry instrumentation. In MALDI MS: A practical guide to instrumentation, methods and applications. New York: Wiley, 29-82.
24. Hopfgartner, G., and E. Varesio. 2005. Application of mass spectrometry for quantitative and qualitative analysis in life sciences. CHIMIA: Int. J. Chem. 59: 321-325.
25. Hopfgartner, G., E. Varesio, V. Tschappat, C. Grivet, E. Bourgogne, and L. A. Leuthold. 2004. Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J. Mass Spectrom. 39: 845-855.
26. Hortin, G. L. 2006. The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin. Chem. 52: 1223-1237.
27. Hoteling, A. J., and K. G. Owens. 2004. Improved PSD and CID on a MALDI TOFMS. J. Am. Soc. Mass Spectrom. 15: 523-535.
28. Hu, Q., R. J. Noll, H. Li, A. Makarov, M. Hardman, and R. G. Cooks. 2005. The orbitrap:A new mass spectrometer. J. Mass Spectrom. 40: 430-443.
29. Hu, Y., S. Zhang, J. Yu, J. Liu, and S. Zheng. 2005. SELDI-TOF-MS: The proteomics and bioinformatics approaches in the diagnosis of breast cancer. The Breast. 14: 250-255.
30. Huang, M. Z., H. J. Hsu, J. Y. Lee, J. Jeng, and J. Shiea. 2006. Direct protein detection from biological media through electrospray-assisted laser desorption ionization/massspectrometry. J. Proteome. Res. 5: 1107-1116.
31. Ifa, D. R., J. M. Wiseman, Q. Song, and R. G. Cooks. 2007. Development of capabilities for imaging mass spectrometry under ambient conditions with desorption electrospray ionization (DESI). Int. J. Mass Spectrom. 259: 8-15.
32. Jenuwein, T. D. A. 2001. Translating the Histone code. Science. 293: 1074-1080.
33. Kelleher, N. L. 2004. Top-down proteomics. Anal. Chem. 76: 197A-203A.
34. Kjeldsen, F., O. B. Hørning, S. S. Jensen, A. M. B. Giessing, and O. N. Jensen. 2008. Towards liquid chromatography time-scale peptide sequencing and characterization of post translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 19: 1156-1162.
35. Klen, T. G., C. M. Andreasen, H. R. Kjeldal, L. R. Leonardsen, T. N. Krogh, P. F. Nielsen, M. V. Sorensen, and O. N. Jensen. 2004. MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports. Anal. Chem. 76: 3576-3583.
36. Laskin, J., and J. H. Futrell. 2005. Activation of large ions in FT-ICR mass spectrometry. Mass Spectrom. Rev. 24: 135-167.
37. Le Blanc, J. C. Y. 2003. Unique scanning capabilities of a new hybrid linear ion trap mass spectrometer (QTRAPTM) used for high sensitivity proteomics applications. Proteomics. 3: 859-869.
38. Loo, J. A., C. G. Edmonds, and R. D. Smith. 1990. Primary sequence information from intact proteins by electrospray ionization tandem mass spectrometry. Science. 248: 201-204.
39. Macek, B., L. F. Waanders, J. V. Olsen, and M. Mann. 2006. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell Proteomics. 5: 949-958.
40. Mackay, C. L., B. Ramsahoye, K. Burgess, K. Cook, S. Weidt, J. Creanor, D. Harrison, P. L. Smith, T. Hupp, and L. Hayward. 2008. Sensitive, specific, and quantitative FTICR mass spectrometry of combinatorial post-translational modifications in intact Histone H4. Anal. Chem. 80: 4147-4153.
41. Madsen, J. A., M. W. Gardner, S. I. Smith, A. R. Ledvina, J. J. Coon, J. C. Schwartz, G. C. Stafford, and J. S. Brodbelt. 2009. Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap. Anal. Chem. 81: 8677-8686.
42. Mathivanan, S., and A. Pandey. 2008. Human proteinpedia as a resource for clinical proteomics. Mol. Cell Proteomics. 7: 2038-2047.
43. McAlister, G. C., D. Phanstiel, D. M. Good, W. T. Berggren, and J. J. Coon. 2007. Implementation of electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer. Anal. Chem. 79: 3525-3534.
44. McLafferty, F. W., K. Breuker, M. Jin, X. Han, G. Infusini, H. Jiang, X. Kong, and T. P. Begley. 2007. Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 274: 6256-6268.
45. Meltretter, J., A. Schmidt, A. Humeny, C. M. Becker, and M. Pischetsrieder. 2008. Analysis of the peptide profile of milk and its changes during thermal treatment and storage. J. Agric. Food Chem. 56: 2899-2906.
46. Miao, Z., and H. Chen. 2009. Direct analysis of liquid samples by desorption electrospray ionization-mass spectrometry (DESI-MS). J. Am. Soc. Mass Spectrom. 20: 10-19.
47. Mihalca, R., Y. E. M. van der Burgt, L. A. McDonnell, D. Marc, C. Iliya, J. R. H. Albert, and M. A. H. Ron. 2006. Combined infrared multiphoton dissociation and electron-capture dissociation using co-linear and overlapping beams in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 20: 1838-1844.
48. Mikesh, L. M., B. Ueberheide, A. Chi, J. J. Coon, J. E. Syka, J. Shabanowitz, and D. F. Hunt. 2006. The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta. 1764: 1811-1822.
49. M'Komaa, A. E., D. L. Bluma, J. L. Norrisb, and T. Koyama. 2007. Detection of preneoplastic and neoplastic prostate disease by MADI profiling of urine. Biochem. Biophys. Res. Commun. 353: 829-834.
50. Molina, H., D. M. Horn, N. Tang, S. Mathivanan, and A. Pandey. 2007. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. PNAS. 104: 2199-2204.
51. Motoyama, A., J. D. Venable, C. I. Ruse, and J. R. Yates. 2006. Automated ultra highpressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal. Chem. 78: 5109-5118.
52. Motoyama, A., and J. R. Yates. 2008. Multidimensional LC separations in shotgun proteomics. Anal. Chem. 80: 7187-7193.
53. Nesvizhskii, A. I., O. Vitek, and R. Aebersold. 2007. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods. 4: 787-797.
54. O'Malley, R. 2002. Life's (more than) a BLASTTM. The Biochemist. 21-23.
55. Ouvry-Patat, S. A., M. P. Torres, C. A. Gelfand, H. H. Quek, M. Easterling, J. P. Speir, and C. H. Borchers. 2009. Top-down proteomics on a high-field Fourier transform ion cyclotron resonance mass spectrometer. Methods Mol. Biol. 492: 215-231.
56. Palagi, P. M., P. Hernandez, D. Walther, and R. D. Appel. 2006. Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics. 6: 5435-5444.
57. Peng, I. X., J. Shiea, R. R. O. Loo, and J. A. Loo. 2007. Electrospray-assisted laser desorption=ionization and tandem mass spectrometry of peptides and proteins. Rapid Commun. Mass Spectrom. 21: 2541-2546.
58. Perkins, D. N., D. J. C. Pappin, D. M. Creasy, and J. S. Cottrell. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 20: 3551-3567.
59. Petricoin, E. F., and L. A. Liotta. 2004. SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr. Opin. Biotechnol. 15: 24-30.
60. Pipes, G. D., P. Campbell, P. V. Bondarenko, B. A. Kerwin, M. J. Treuheit, and H. S. Gadgil. 2010. Middle-down fragmentation for the identification and quantitation of site specific methionine oxidation in an IgG1 molecule. J. Pharm. Sci. 99(11): 4469-4476.
61. Poon, T. C. W. 2007. Opportunities and limitations of SELDI-TOF-MS in biomedical research: Practical advices. Expert Rev. Proteomics. 4: 51-65.
62. Qian, W. J., D. G. Camp, and R. D. Smith. 2004. High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry. Expert Rev. Proteomics. 1: 87-95.
63. Raspopov, S. A., A. El-Faramawy, B. A. Thomson, and K. W. M. Siu. 2006. Infrared multiphoton dissociation in quadrupole time-of-flight mass spectrometry: Top-down characterization of proteins. Anal. Chem. 78: 4572-4577.
64. Renfrow, M. B., H. J. Cooper, M. Tomana, R. Kulhavy, Y. Hiki, K. Toma, M. R. Emmett, J. Mestecky, A. G. Marshall, and J. Novak. 2005. Determination of aberranto glycosylation in the IgA1 hinge region by electron capture dissociation Fourier transformion cyclotron resonance mass spectrometry. J. Biol. Chem. 280: 19136-19145.
65. Resing, K. A., and N. G. Ahn. 2005. Proteomics strategies for protein identification. FEBS Lett. 579: 885-889.
66. Reyzer, M. L., and R. M. Caprioli. 2005. MALDI mass spectrometry for direct tissue analysis: A new tool for biomarker discovery. J. Proteome. Res. 4: 1138-1142.
67. Ryu, O. H., J. C. Atkinson, G. T. Hoehn, G. G. Illei, and T. C. Hart. 2006. Identification of parotid salivary biomarkers in Sjögren's syndrome by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry and two-dimensional difference gel electrophoresis. Rheumatology. 45: 1077-1086.
68. Schwartz, J. C., M. W. Senko, and J. E. P. Syka. 2002. A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass. Spectrom. 13: 659-669.
69. Searle, B. C. 2010. Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics. 10: 1265-1269.
70. Shiea, J., M. Z. Huang, H. J. Hsu, C. Y. Lee, C. H. Yuan, I. Beech, and J. Sunner. 2005. Electrospray-assisted laser desorption/ionization mass spectrometry for direct ambient analysis of solids. Rapid Commun. Mass Spectrom. 19: 3701-3704.
71. Sihlbom, C. 2004. Glycoproteomics of cerebrospinal fluid in neurodegenerative disease. Int. J. Mass Spectrom. 234: 145-152.
72. Simpkins, F., J. A. Czechowicz, L. Liotta, and E. C. Kohn. 2005. SELDI-TOF mass spectrometry for cancer biomarker discovery and serum proteomic diagnostics. Pharmacogenomics. 6: 647-653.
73. Siuti, N., and N. L. Kelleher. 2007. Decoding protein modifications using top-down mass spectrometry. Nat. Methods. 4: 817-821.
74. Steen, H., and M. Mann. 2004. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5: 699-711.
75. Syka, J. E., J. J. Coon, M. J. Schroeder, J. Shabanowitz, and D. F. Hunt. 2004. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. 101: 9528-9533.
76. Tabb, D. L., C. G. Fernando, and M. C. Chambers. 2007. MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 6: 654-661.
77. Taká ts, Z., J. M. Wiseman, and R. G. Cooks. 2005. Ambient mass spectrometry using desorption electrospray ionization (DESI): Instrumentation, mechanisms and applications in forensics, chemistry, and biology. J. Mass Spectrom. 40: 1261-1275.
78. Taká ts, Z., J. M. Wiseman, B. Gologan, and R. G. Cooks. 2004. Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science. 306: 471-473.
79. Tanaka, K., H. Waki, Y. Ido, S. Akita, Y. Yoshida, T. Yoshida, and T. Matsuo. 2005. Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2: 151-153.
80. Tang, N., P. Tornatore, and S. R. Weinberger. 2004. Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23: 34-44.
81. Tanner, S., H. Shu, A. Frank, L. C. Wang, E. Zandi, M. Mumby, P. A. Pevzner, and V. Bafna. 2005. InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 77: 4626-4639.
82. Thiede, B., W. Höhenwarter, A. Krah, J. Mattow, M. Schmid, F. Schmidt, and P. R. Jungblut. 2005. Peptide mass fingerprinting. Methods. 35: 237-247.
83. Tsai, Y. S., A. Scherl, J. L. Shaw, C. L. MacKay, S. A. Shaffer, P. R. Langridge-Smith, and D. R. Goodlett. 2009. Precursor ion independent algorithm for top-down shotgun proteomics. J. Am. Soc. Mass Spectrom. 20: 2154-2166.
84. Twerenbold, D., D. Gerber, D. Gritti, Y. Gonin, A. Netuschill, F. Rossel, D. Schenker, and J. L. Vuilleumier. 2001. Single molecule detector for mass spectrometry with mass independent detection efficiency. Proteomics. 1: 66-69.
85. Venter, A., and R. G. Cooks. 2007. Desorption electrospray ionization in a small pressure-tight enclosure. Anal. Chem. 79: 6398-6403.
86. Vestal, M. L., and J. M. Campbell. 2005. Tandem time-of-flight mass spectrometry. Methods Enzymol. 402: 79-108.
87. Voortman, J., T. V. Pham, J. C. Knol, G. Giaccone, and C. R. Jimenez. 2008. Time course MALDI-TOF-MS serum peptide profiling of non-small cell lung cancer patients treated with bortezomib, cisplatin and gemcitabine. J. Clin. Oncol. 26: 8007.
88. Watson, J. T. 2007. "Top Down" Analysis of proteins for the masses. Int. J. Appl. Sci. Eng. 5: 81-95.
89. Watt, S. J., M. M. Sheil, J. L. Beck, P. Prosselkov, G. Otting, and N. E. Dixon. 2007. Effect of protein stabilization on charge state distribution in positive- and negative-ion electrospray ionization mass spectra. J. Am. Soc. Mass Spectrom. 18: 1605-1611.
90. Wisniewski, J. R., A. Zougman, S. Krü ger, and M. Mann. 2007. Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue. Mol. Cell Proteomics. 6: 72-87.
91. Wu, J., C. S. Hughes, P. Picard, S. Letarte, M. Gaudreult, J. F. Levesque, D. A. Nicoll-Griffith, and K. P. Bateman. 2007. High-throughput cytochrome P450 inhibition assays using laser diode thermal desorption-atmospheric pressure chemical ionizationtandem mass spectrometry. Anal. Chem. 79: 4657-4665.
92. Wu, S., H. Amato, R. Biringer, G. Choudhary, P. Shieh, and W. S. Hancock. 2002. Targeted proteomics of low-level proteins in human plasma by LC/MSn: Using human growth hormone as a model system. J. Proteome Res. 1: 459-465.
93. Wuhrer, M., M. I. Catalina, A. M. Deelder, and C. H. Hokke. 2007. Glycoproteomics based on tandem mass spectrometry of glycopeptides. J. Chromatogr. B. 849: 115-128.
94. Xu, P., and J. Peng. 2008. Characterization of polyubiquitin chain structure by middle down mass spectrometry. Anal. Chem. 80: 3438-3444.
95. Yocum, A. K., and A. M. Chinnaiyan. 2009. Current affairs in quantitative targeted proteomics: Multiple reaction monitoring-mass spectrometry. Brief. Functional Genomics Proteomics. 8: 145-157.
96. Zappacosta, F., T. S. Collingwood, M. J. Huddleston, and R. S. Annan. 2006. A quantitative results-driven approach to analyzing multisite protein phosphorylation. Mol. Cell Proteomics. 5: 2019-2030.
97. Zhang, H., B. Kong, X. Qu, L. Jia, B. Deng, and Q. Yang. 2006. Biomarker discovery for ovarian cancer using SELDI-TOF-MS. Gynecol. Oncol. 102: 61-66.
98. Zhang, Z. 2004. Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 76: 3908-3922.
99. Zubarev, R. A. 2003. Reactions of poly peptides with electrons in gas phase. Mass. Spectrom. Rev. 22: 57-77.
100. Zubarev, R. A. 2009. Electron capture dissociation LC/MS/MS for bottom-up proteomics. Methods Mol. Biol. 492: 413-416.