Understanding and optimizing electrospray ionization techniques for proteomic analysis

Expert Review of Proteomics

Volumn 8, Issue 2, 2011, Pages 197-209

  Liuni, Peter ^a   Wilson, Derek J ^a,b  

^a YORK UNIVERSITY   (Canada)

^b Center for Research in Mass Spectrometry   (Canada)

Author keywords

capillary electrophoresis; CE; CE MS; electrospray ionization; ESI; ESI MS; LC; LC MS; liquid chromatography; mass spectrometry; optimization; proteomics

Indexed keywords

SOLVENT;

ACCURACY; CAPILLARY ELECTROPHORESIS; ELECTROSPRAY MASS SPECTROMETRY; ELUTION; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW;

ANIMALS; HUMANS; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 79955051648     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.10.111     Document Type: Review

References (94)

1. Koichi T, Hiroaki W, Yutaka I et al. Protein and polymer analyses up to m/z 100,000 by laser ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 2(8), 151-153 (1988).
2. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10000 daltons. Anal. Chem. 60(20), 2299-2301 (1988).
3. Yamashita M, Fenn JB. Electrospray ion-source - another variation on the free-jet theme. J. Phys. Chem. 88(20), 4451-4459 (1984).
4. Dole M, Mack LL, Hines RL. Molecular beams of macroions. J. Chem. Phys. 49(5), 2240-2250 (1968).
5. Loo J. Teaching editorial - bioanalytical mass spectrometry: many flavors to choose. Bioconjugate Chem. 6(6), 644-665 (1995).
6. Loo JA, Udseth HR, Smith RD. Peptide and protein-analysis by electrospray ionization mass-spectrometry and capillary electrophoresis mass-spectrometry. Anal. Biochem. 179(2), 404-412 (1989). (Pubitemid 19153856)
7. McCloskey JA, Crain PF. Progress in mass-spectrometry of nucleic-acid constituents - analysis of xenobiotic modifications and measurements at high mass. Int. J. Mass Spectrom. Ion Process. 118, 593-615 (1992).
8. Huang EC, Pramanik BN, Tsarbopoulos A et al. Application of electrospray mass-spectrometry in probing protein-protein and protein-ligand noncovalent interactions. J. Am. Soc. Mass Spectrom. 4(8), 624-630 (1993).
9. Hughey CA, Rodgers RP, Marshall AG. Resolution of 11,000 compositionally distinct components in a single electrospray ionization Fourier transform ion cyclotron resonance mass spectrum of crude oil. Anal. Chem. 74(16), 4145-4149 (2002). (Pubitemid 34912915)
10. Chen GD, Pramanik BN. LC-MS for protein characterization: current capabilities and future trends. Expert Rev. Proteomics 5(3), 435-444 (2008). (Pubitemid 351871119)
11. Wang H, Hanash S. Multi-dimensional liquid phase based separations in proteomics. J. Chromatogr B Analyt. Technol. Biomed. Life Sci. 787(1), 11-18 (2003). (Pubitemid 36351262)
12. Whitehouse CM, Dreyer RN, Yamashita M et al. Electrospray interface for liquid chromatographs and mass spectrometers. Anal. Chem. 57(3), 675-679 (1985). (Pubitemid 15479593)
13. Peschke M, Verkerk UH, Kebarle P. Features of the ESI mechanism that affect the observation of multiply charged noncovalent protein complexes and the determination of the association constant by the titration method. J. Am. Soc. Mass Spectrom. 15(10), 1424-1434 (2004). (Pubitemid 39311693)
14. Verkerk U, Kebarle P. On the mechanism of electrospray ionization mass spectrometry. In:Electrospray and MALDI Mass Spectrometry (2nd Edition) . Cole RB (Ed.). John Wiley & Sons Inc., NJ, USA, 3-48 (2010).
15. Kebarle P. A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. J. Mass Spectrom. 35(7), 804-817 (2000). (Pubitemid 30479522)
16. Taylor GI, McEwan AD. Stability of a horizontal fluid interface in a vertical electric field. J. Fluid Mech. 22(1) 1-15 (1965).
17. Smith JN, Flagan RC, Beauchamp JL. Droplet evaporation and discharge dynamics in electrospray ionization. J. Phys. Chem. A 106(42), 9957-9967 (2002). (Pubitemid 35410170)
18. Rayleigh. On the equilibrium of liquid conducting masses charged with electricity. Philos. Mag. 5 14(87), 184-186 (1882).
19. Gomez A, Tang KQ. Charge and fission of droplets in electrostatic sprays. Phys. Fluids 6(1), 404-414 (1994).
20. Taflin DC, Ward TL, Davis EJ. Electrified droplet fission and the Rayleigh limit. Langmuir 5(2), 376-384 (1989)
21. Schmelzeisenredeker G, Butfering L, Rollgen FW. Desolvation of ions and molecules in thermospray mass-spectrometry. Int. J. Mass Spectrom. Ion Process. 90(2), 139-150 (1989).
22. Iribarne JV, Thomson BA. Evaporation of small ions from charged droplets. J. Chem. Phys. 64(6), 2287-2294 (1976).
23. Thomson BA, Iribarne JV. Field-induced ion evaporation from liquid surfaces at atmospheric-pressure. J. Chem. Phys. 71(11), 4451-4463 (1979).
24. Loscertales IG, Delamora JF. Experiments on the kinetics of field evaporation of small ions from droplets. J. Chem. Phys. 103(12), 5041-5060 (1995).
25. de la Mora JF. Electrospray ionization of large multiply charged species proceeds via Dole's charged residue mechanism. Anal. Chim. Acta 406(1), 93-104 (2000).
26. Konermann LA. Minimalist model for exploring conformational effects on the electrospray charge state distribution of proteins. J. Phys. Chem. B 111(23), 6534-6543 (2007).
27. Hogan CJ, Carroll JA, Rohrs HW et al. Combined charged residue-field emission model of macromolecular electrospray ionization. Anal. Chem. 81(1), 369-377 (2009).
28. Chech NB, Enke CG. Selectivity in electrospray ionization mass spectrometry. In:Electrospray and MALDI Mass Spectrometry (2nd Edition). Cole RB (Ed.). John Wiley & Sons Inc., NJ, USA, 49-73 (2010).
29. Cech NB, Enke CG. Relating electrospray ionization response to nonpolar character of small peptides. Anal. Chem. 72(13), 2717-2723 (2000). (Pubitemid 30452234)
30. Kaltashov IA, Mohimen A. Estimates of protein surface areas in solution by electrospray ionization mass spectrometry. Anal. Chem. 77(16), 5370-5379 (2005). (Pubitemid 41140859)
31. Lavarone AT, Williams ER. Mechanism of charging and supercharging molecules in electrospray ionization. J. Am. Chem. Soc. 125(8), 2319-2327 (2003). (Pubitemid 36245725)
32. Winger BE, Lightwahl KJ, Loo RRO et al. Observation and implications of high mass-to-charge ratio ions from electrospray mass spectrometry. J. Am. Soc. Mass Spectrom. 4(7), 536-545 (1993).
33. Kebarle P, Verkerk UH. Electrospray: from ions in solution to ions in the gas phase, what we know. Mass Spectrom. Rev. 28(6), 898-917 (2009).
34. Samalikova M, Grandori R. Protein charge-state distributions in electrospray-ionization mass spectrometry do not appear to be limited by the surface tension of the solvent. J. Am. Chem. Soc. 125(44), 13352-13353 (2003). (Pubitemid 37352109)
35. Allen MH, Vestal ML. Design and performance of a novel electrospray interface. J. Am. Soc. Mass Spectrom. 3(1), 18-26 (1992).
36. Bruins AP. Mass-spectrometry with ion sources operating at atmospheric-pressure. Mass Spectrom. Rev. 10(1), 53-77 (1991).
37. Korner R, Wilm M, Morand K et al. Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests. J. Am. Soc. Mass Spectrom. 7(2), 150-156 (1996). (Pubitemid 26099224)
38. Maziarz EP, Baker GA, Mure JV et al. A comparison of electrospray versus nanoelectrospray ionization Fourier transform mass spectrometry for the analysis of synthetic poly(dimethylsiloxane)/poly(ethylene glycol) oligomer blends. Int. J. Mass Spectrom. 202(1-3), 241-250 (2000).
39. Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. Anal. Chem. 68(1), 1-8 (1996).
40. Wilm M, Shevchenko A, Houthaeve T et al. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379(6564), 466-469 (1996).
41. Wood TD, Moy MA, Dolan AR et al. Miniaturization of electrospray ionization mass spectrometry. Appl. Spectrosc. Rev. 38(2), 187-244 (2003).
42. Davis MT, Stahl DC, Hefta SA et al. A microscale electrospray interface for online, capillary liquid-chromatography tandem mass-spectrometry of complex peptide mixtures. Anal. Chem. 67(24), 4549-4556 (1995). (Pubitemid 26020787)
43. Gatlin CL, Kleemann GR, Hays LG et al. Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography microspray and nanospray mass spectrometry. Anal. Biochem. 263(1), 93-101 (1998). (Pubitemid 28445431)
44. Niessen WMA. State-of-the-art in liquid chromatography-mass spectrometry. J. Chromatogr. A. 856(1-2), 179-197 (1999). (Pubitemid 29436011)
45. Kostiainen R, Kotiaho T, Kuuranne T et al. Liquid chromatography/ atmospheric pressure ionization-mass spectrometry in drug metabolism studies. J. Mass Spectrom. 38(4), 357-372 (2003). (Pubitemid 36582213)
46. Xu RNX, Fan LM, Rieser MJ et al. Recent advances in high-throughput quantitative bioanalysis by LC-MS/MS. J. Pharm. Biomed. Anal. 44(2), 342-355 (2007). (Pubitemid 46880094)
47. Petrovic M, Hernando MD, Diaz-Cruz MS et al. Liquid chromatography-tandem mass spectrometry for the analysis of pharmaceutical residues in environmental samples: a review. J. Chromatogr. A 1067(1-2), 1-14 (2005). (Pubitemid 40363388)
48. Lazar AC, Wang LT, Blattler WA et al. Analysis of the composition of immunoconjugates using size-exclusion chromatography coupled to mass spectrometry. Rapid Commun. Mass Spectrom. 19(13), 1806-1814 (2005). (Pubitemid 40886704)
49. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003). (Pubitemid 36362757)
50. Nagele E, Vollmer M, Horth P et al. 2D-LC/MS techniques for the identification of proteins in highly complex mixtures. Expert Rev. Proteomics 1(1), 37-46 (2004). (Pubitemid 43826427)
51. Peng JM, Elias JE, Thoreen CC et al. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2(1), 43-50 (2003). (Pubitemid 36207189)
52. Garcia MC. The effect of the mobile phase additives on sensitivity in the analysis of peptides and proteins by high-performance liquid chromatography-electrospray mass spectrometry. J. Chromatogr. B. 825(2), 111-123 (2005). (Pubitemid 41423594)
53. Ishihama Y, Katayama H, Asakawa N. Surfactants usable for electrospray ionization mass spectrometry. Anal. Biochem. 287(1), 45-54 (2000).
54. Smith RD, Olivares JA, Nguyen NT et al. Capillary zone electrophoresis mass-spectrometry using an electrospray ionization interface. Anal. Chem. 60(5), 436-441 (1988). (Pubitemid 18059805)
55. Schmitt-Kopplin P, Frommberger M. Capillary electrophoresis - mass spectrometry: 15 years of developments and applications. Electrophoresis 24(22-23), 3837-3867 (2003). (Pubitemid 38094442)
56. Wang SH, Regnier FE. Proteolysis of whole cell extracts with immobilized enzyme columns as part of multidimensional chromatography. J. Chromatogr. A 913(1-2), 429-436 (2001). (Pubitemid 32261009)
57. McLafferty FW, Breuker K, Jin M et al. Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J. 274(24), 6256-6268 (2007). (Pubitemid 350215920)
58. Bogdanov B, Smith RD. Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom. Rev. 24(2), 168-200 (2005). (Pubitemid 40328973)
59. Tang K, Page JS, Smith RD. Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 15(10), 1416-1423 (2004). (Pubitemid 39311692)
60. Winter D, Seidler J, Ziv-Lehrman S et al. Simultaneous identification and quantification of proteins by differential O-16/O-18 labeling and UPLC-MS/MS applied to mouse cerebellar phosphoproteome following irradiation. Anticancer Res. 29(12), 4949-4958 (2009).
61. Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19(3), 242-247 (2001). (Pubitemid 32220565)
62. Wolters DA, Washburn MP, Yates JR. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73(23), 5683-5690 (2001). (Pubitemid 33126725)
63. Mitulovic G, Stingl C, Smoluch M et al. Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics 4(9), 2545-2557 (2004). (Pubitemid 39202156)
64. Marginean I, Kelly RT, Moore RJ et al. Selection of the optimum electrospray voltage for gradient elution LC-MS measurements. J. Am. Soc. Mass Spectrom. 20(4), 682-688 (2009).
65. Tang L, Kebarle P. Effect of the conductivity of the electrosprayed solution on the electrospray current - factors determining analyte sensitivity in electrospray mass spectrometry. Anal. Chem. 63(23), 2709-2715 (1991).
66. Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA et al. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl Acad. Sci. USA 104(14), 5860-5865 (2007). (Pubitemid 47175624)
67. Peng JM, Gygi SP. Proteomics: the move to mixtures. J. Mass Spectrom. 36(10), 1083-1091 (2001). (Pubitemid 33040761)
68. Kelleher NL. Top-down proteomics. Anal. Chem. 76(11), 196A-203A (2004).
69. Ge Y, Lawhorn BG, ElNaggar M et al. Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc. 124(4), 672-678 (2002). (Pubitemid 34101174)
70. Wang YJ, Balgley BM, Rudnick PA et al. Integrated capillary isoelectric focusing/ nano-reversed phase liquid chromatography coupled with ESI-MS for characterization of intact yeast proteins. J. Proteome Res. 4(1), 36-42 (2005). (Pubitemid 40344455)
71. Collier TS, Hawkridge AM, Georgianna DR et al. Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal. Chem. 80(13), 4994-5001 (2008). (Pubitemid 351956307)
72. Han XM, Jin M, Breuker K et al. Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 314(5796), 109-112 (2006). (Pubitemid 44547751)
73. Lomeli SH, Yin S, Loo RRO et al. Increasing: charge while preserving noncovalent protein complexes for ESI-MS. J. Am. Soc. Mass Spectrom. 20(4), 593-596 (2009).
74. Vellaichamy A, Tran JC, Catherman AD et al. Size-sorting combined with improved nanocapillary liquid chromatography-mass spectrometry for identification of intact proteins up to 80 kDa. Anal. Chem. 82(4), 1234-1244 (2010).
75. Lee JE, Kellie JF, Tran JC et al. A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J. Am. Soc. Mass Spectrom. 20(12), 2183-2191 (2009).
76. Meng FY, Du Y, Miller LM et al. Molecular-level description of proteins from Saccharomyces cerevisiae using quadrupole FT hybrid mass spectrometry for top down proteomics. Anal. Chem. 76(10), 2852-2858 (2004). (Pubitemid 38657712)
77. Jensen PK, Pasa-Tolic L, Anderson GA et al. Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 71(11), 2076-2084 (1999). (Pubitemid 29256884)
78. Botelho D, Wall MJ, Vieira DB et al. Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation. J. Proteome Res. 9(6), 2863-2870 (2010).
79. Nemeth-Cawley JF, Tangarone BS, Rouse JC. 'Top down' characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. J. Proteome Res. 2(5), 495-505 (2003). (Pubitemid 37376844)
80. Simpson DC, Ahn S, Pasa-Tolic L et al. Using size exclusion chromatography- RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 27(13), 2722-2733 (2006). (Pubitemid 44057522)
81. Schlautman J, Rozek W, Stetler R et al. Multidimensional protein fractionation using ProteomeLab PF 2DTM for profiling amyotrophic lateral sclerosis immunity: a preliminary report. Proteome Sci. 6(1), 26 (2008).
82. Ros A, Faupel M, Mees H et al. Protein purification by off-gel electrophoresis. Proteomics 2(2), 151-156 (2002). (Pubitemid 34273084)
83. Tran JC, Doucette AA. Multiplexed size separation of intact proteins in solution phase for mass spectrometry. Anal. Chem. 81(15), 6201-6209 (2009).
84. Tran JC, Doucette AA. Gel-eluted liquid fraction entrapment electrophoresis: an electrophoretic method for broad molecular weight range proteome separation. Anal. Chem. 80(5), 1568-1573 (2008). (Pubitemid 351429561)
85. Wu WW, Wang GH, Baek SJ et al. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res. 5(3), 651-658 (2006). (Pubitemid 43364106)
86. Wiese S. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 7(3), 340-350 (2007). (Pubitemid 46293976)
87. Ross PL, Huang YLN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3(12), 1154-1169 (2004).
88. Hansen KC, Schmitt-Ulms G, Chalkley RJ et al. Mass spectrometric analysis of protein mixtures at low levels using cleavable C-13-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell. Proteomics 2(5), 299-314 (2003).
89. Old WM, Meyer-Arendt K, Aveline-Wolf L et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 4(10), 1487-1502 (2005). (Pubitemid 41555475)
90. Bondarenko PV, Chelius D, Shaler TA. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 74(18), 4741-4749 (2002).
91. Wang WX, Zhou HH, Lin H et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75(18), 4818-4826 (2003). (Pubitemid 37139783)
92. Callister SJ, Barry RC, Adkins JN et al. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J. Proteome Res. 5(2), 277-286 (2006). (Pubitemid 43222296)
93. Valaskovic GA, Murphy JP, Lee MS. Automated orthogonal control system for electrospray ionization. J. Am. Soc. Mass Spectrom. 15(8), 1201-1215 (2004). (Pubitemid 38970064)
94. Gapeev A, Berton A, Fabris D. Current-controlled nanospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 20(7), 1334-1341 (2009).