Compelling advantages of negative ion mode detection in high-mass maldi-ms for homomeric protein complexes

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 2, 2012, Pages 213-224

  Mädler, Stefanie ^a   Barylyuk, Konstantin ^a   Boeri Erba, Elisabetta ^a   Nieckarz, Robert J ^a   Zenobi, Renato ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Chemical cross linking; MALDI TOF MS; Multiply charged ions; NHS ester

Indexed keywords

CHARGED ANIONS; CHARGED SPECIES; CHEMICAL CROSS-LINKING; CROSS-LINKED COMPLEX; CROSS-LINKED PROTEINS; INSTRUMENTAL PARAMETERS; MALDI-MASS SPECTROMETRY; MALDI-MS; MALDI-TOF-MS; MATRIX; MODE DETECTION; MULTIMERS; MULTIPLY CHARGED ANIONS; MULTIPLY CHARGED IONS; NONCOVALENT; POSITIVE ION MODE; PROTEIN COMPLEXES; PROTEIN-PROTEIN INTERACTIONS; RAPID IDENTIFICATION; REPRODUCIBILITIES; SAMPLE PREPARATION; SINAPINIC ACID; SOLUTION PHASE;

CHEMICAL DETECTION; CROSSLINKING; MASS SPECTROMETRY; POSITIVE IONS; PROTEINS; STOICHIOMETRY;

NEGATIVE IONS;

BETA LACTOGLOBULIN; CITRATE SYNTHASE; CONCANAVALIN A; CREATINE KINASE; FRUCTOSE BISPHOSPHATE ALDOLASE; GLUTATHIONE TRANSFERASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GLYCOGEN PHOSPHORYLASE B; IMMUNOGLOBULIN G; LYSOZYME; MYOGLOBIN; PYRUVATE KINASE; RIBONUCLEASE A; SINAPIC ACID; TRYPSINOGEN;

ANALYTICAL PARAMETERS; ARTICLE; COMPLEX FORMATION; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; LASER POWER; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NEGATIVE ION MODE MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PH; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; SAMPLE; SIGNAL NOISE RATIO;

ANIMALS; ANIONS; CATTLE; CHICKENS; HORSES; HYDROGEN-ION CONCENTRATION; PHOSPHATES; PROTEIN CONFORMATION; PROTEIN SUBUNITS; PROTEINS; RABBITS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84856274818     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-011-0274-x     Document Type: Article

References (52)

1. DS Goodsell AJ Olson 2000 Structural symmetry and protein function Annu. Rev. Biophys. Biomol. Struct. 29 105 153 10.1146/annurev.biophys.29.1.105 1:CAS:528:DC%2BD3cXlsFOntbk%3D (Pubitemid 30599590)
2. RH van den Heuvel AJ Heck 2004 Native protein mass spectrometry: from intact oligomers to functional machineries Curr. Opin. Chem. Biol. 8 519 526 10.1016/j.cbpa.2004.08.006 (Pubitemid 39278349)
3. AJR Heck RHH van den Heuvel 2004 Investigation of intact protein complexes by mass spectrometry Mass Spectrom. Rev. 23 368 389 10.1002/mas.10081 1:CAS:528:DC%2BD2cXns1Gqsbw%3D
4. H Hernandez CV Robinson 2007 Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry Nat. Protocol. 2 715 726 10.1038/nprot.2007.73 1:CAS:528:DC%2BD2sXhtFGntbfP (Pubitemid 47040033)
5. RK Chitta DL Rempel ML Gross 2005 Determination of affinity constants and response factors of the noncovalent dimer of gramicidin by electrospray ionization mass spectrometry and mathematical modeling J. Am. Soc. Mass Spectrom. 16 1031 1038 10.1016/j.jasms.2005.04.001 1:CAS:528: DC%2BD2MXlsFCks7s%3D (Pubitemid 40828784)
6. JJ Liu L Konermann 2011 Protein-protein binding affinities in solution determined by electrospray mass spectrometry J. Am. Soc. Mass Spectrom. 22 408 417 10.1007/s13361-010-0052-1 1:CAS:528:DC%2BC3MXnt1OitLo%3D
7. A Ayed AN Krutchinsky W Ens KG Standing HW Duckworth 1998 Quantitative evaluation of protein-protein and ligand-protein equilibria of a large allosteric enzyme by electrospray ionization time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 12 339 344 10.1002/(SICI)1097-0231(19980415)12: 7<339::AID-RCM163>3.0.CO;2-6 1:CAS:528:DyaK1cXisVWjsr0%3D (Pubitemid 28178509)
8. TB Farmer RM Caprioli 1991 Assessing the multimeric states of proteins: Studies using laser desorption mass spectrometry Biol. Mass Spectrom. 20 796 800 10.1002/bms.1200201209 1:CAS:528:DyaK38XlsVyqtw%3D%3D
9. TB Farmer RM Caprioli 1998 Determination of protein-protein interactions by matrix-assisted laser desorption/ionization mass spectrometry J. Mass Spectrom. 33 697 704 10.1002/(SICI)1096-9888(199808)33:8<697::AID- JMS711>3.0.CO;2-H 1:CAS:528:DyaK1cXmtVCju70%3D (Pubitemid 28380337)
10. A Nazabal R Wenzel R Zenobi 2006 Immunoassays with direct mass spectrometric detection Anal. Chem. 78 3562 3570 10.1021/ac0519108 1:CAS:528:DC%2BD28XktFeisb8%3D (Pubitemid 43848946)
11. T Pimenova CP Pereira DJ Schaer R Zenobi 2009 Characterization of high molecular weight multimeric states of human haptoglobin and hemoglobin-based oxygen carriers by high-mass MALDI MS J. Sep. Sci. 32 1224 1230 10.1002/jssc.200800625 1:CAS:528:DC%2BD1MXlvVCltrY%3D
12. BA Budnik SC Moyer JL Pittman VB Ivleva U Sommer CE Costello PB O'Connor 2004 High pressure MALDI-FTMS: Implications for proteomics Int. J. Mass Spectrom. 234 203 212 10.1016/j.ijms.2004.02.011 1:CAS:528:DC%2BD2cXktVWitbg%3D
13. PB O'Connor CE Costello 2001 A high pressure matrix-assisted laser desorption/ionization fourier transform mass spectrometry ion source for thermal stabilization of labile biomolecules Rapid Commun. Mass Spectrom. 15 1862 1868 10.1002/rcm.447 (Pubitemid 32927761)
14. J Zhou T Lee 1995 Charge state distribution shifting of protein ions observed in matrix-assisted laser desorption ionization mass spectrometry J. Am. Soc. Mass Spectrom. 6 1183 1189 10.1016/1044-0305(95)00578-1 1:CAS:528:DyaK28XhtVKltw%3D%3D
15. AS Kononikhin EN Nikolaev V Frankevich R Zenobi 2005 Letter: Multiply charged ions in matrix-assisted laser desorption/ionization generated from electrosprayed sample layers Eur. J. Mass Spectrom. 11 257 259 10.1255/ejms.729 1:CAS:528:DC%2BD2MXhtF2gt7fM (Pubitemid 41241570)
16. V Frankevich J Zhang M Dashtiev R Zenobi 2003 Production and fragmentation of multiply charged ions in "electron-free" matrix-assisted laser desorption/ionization Rapid Commun. Mass Spectrom. 17 2343 2348 10.1002/rcm.1194 1:CAS:528:DC%2BD3sXotlGnurg%3D (Pubitemid 37243320)
17. VE Frankevich J Zhang SD Friess M Dashtiev R Zenobi 2003 Role of electrons in laser desorption/ionization mass spectrometry Anal. Chem. 75 6063 6067 10.1021/ac034436j 1:CAS:528:DC%2BD3sXot1Khsb0%3D (Pubitemid 37420595)
18. MV Gorshkov VE Frankevich R Zenobi 2002 Characteristics of photoelectrons emitted in matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance experiments Eur. J. Mass Spectrom. 8 67 69 10.1255/ejms.474 1:CAS:528:DC%2BD38Xis1Kjtbk%3D
19. TJD Jorgensen G Bojesen H Rahbek-Nielsen 1998 The proton affinities of seven matrix-assisted laser desorption/ionization matrices correlated with the formation of multiply charged ions Eur. J. Mass Spectrom. 4 39 45 10.1255/ejms.189 1:CAS:528:DyaK1cXktVWru78%3D
20. M Karas R Kruger 2003 Ion formation in MALDI: The cluster ionization mechanism Chem. Rev. 103 427 440 10.1021/cr010376a 1:CAS:528: DC%2BD3sXksFKhtw%3D%3D
21. ST Tsai CW Chen LCL Huang MC Huang CH Chen YS Wang 2006 Simultaneous mass analysis of positive and negative ions using a dual-polarity time-of-flight mass spectrometer Anal. Chem. 78 7729 7734 10.1021/ac061213v 1:CAS:528:DC%2BD28XhtVyhtr7L (Pubitemid 44788716)
22. S Alves F Fournier C Afonso F Wind JC Tabet 2006 Gas-phase ionization/desolvation processes and their effect on protein charge state distribution under matrix-assisted laser desorption/ionization conditions Eur. J. Mass Spectrom. 12 369 383 10.1255/ejms.822 1:CAS:528:DC%2BD2sXktVOjtbw%3D
23. PY Yau TW Dominic Chan PG Cullis AW Colburn PJ Derrick 1993 Threshold fluences for production of positive and negative ions in matrix-assisted laser desorption/ionisation using liquid and solid matrices Chem. Phys. Lett. 202 93 100 10.1016/0009-2614(93)85356-S 1:CAS:528:DyaK3sXis1ehs70%3D
24. M Dashtiev E Wafler U Rohling M Gorshkov F Hillenkamp R Zenobi 2007 Positive and negative analyte ion yield in matrix-assisted laser desorption/ionization Int. J. Mass Spectrom. 268 122 130 10.1016/j.ijms.2007.07. 001 1:CAS:528:DC%2BD2sXht1ymsr%2FN
25. M Karas M Glückmann J Schäfer 2000 Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors J. Mass Spectrom. 35 1 12 10.1002/(SICI)1096-9888(200001)35: 1<1::AID-JMS904>3.0.CO;2-0 1:CAS:528:DC%2BD3cXhtVans7g%3D (Pubitemid 30060147)
26. R Knochenmuss A Stortelder K Breuker R Zenobi 2000 Secondary ion-molecule reactions in matrix-assisted laser desorption/ionization J. Mass Spectrom. 35 1237 1245 10.1002/1096-9888(200011)35:11<1237::AID-JMS74>3.0.CO;2-O 1:CAS:528:DC%2BD3cXosl2mtbk%3D
27. R Knochenmuss 2003 A quantitative model of ultraviolet matrix-assisted laser desorption/ionization including analyte ion generation Anal. Chem. 75 2199 2207 10.1021/ac034032r 1:CAS:528:DC%2BD3sXivFagur8%3D (Pubitemid 36582799)
28. R Knochenmuss 2002 A quantitative model of ultraviolet matrix-assisted laser desorption/ionization J. Mass Spectrom. 37 867 877 10.1002/jms.349 1:CAS:528:DC%2BD38XmvFOjtr0%3D (Pubitemid 35012526)
29. R Knochenmuss 2009 A bipolar rate equation model of MALDI primary and secondary ionization processes, with application to positive/negative analyte ion ratios and suppression effects Int. J. Mass Spectrom. 285 105 113 10.1016/j.ijms.2009.05.002 1:CAS:528:DC%2BD1MXoslejsb4%3D
30. TW Jaskolla M Karas 2011 Compelling evidence for lucky survivor and gas phase protonation: The unified MALDI analyte protonation mechanism J. Am. Soc. Mass Spectrom. 22 976 988 10.1007/s13361-011-0093-0 1:CAS:528: DC%2BC3MXnt1Ohsrc%3D
31. BH Liu YT Lee YS Wang 2009 Incoherent production reactions of positive and negative ions in matrix-assisted laser desorption/ionization J. Am. Soc. Mass Spectrom. 20 1078 1086 10.1016/j.jasms.2009.02.012 1:CAS:528: DC%2BD1MXmtVehu7w%3D
32. Hillenkamp, F.; Nazabal, A.; Roehling, U.; Wenzel, R.: Method for analyzing ions of high mass in time-of-flight mass spectrometer, involves applying potential difference between front and back sides of electron multiplier to multiply number of electrons. WO2009086642-A1 WOCH000007 04 Jan 2008
33. AJ Lomant G Fairbanks 1976 Chemical probes of extended biological structures: Synthesis and properties of the cleavable protein cross-linking reagent [35S]Dithiobis(succinimidyl propionate) J. Mol. Biol. 104 243 261 10.1016/0022-2836(76)90011-5 1:CAS:528:DyaE28XksF2isbs%3D
34. C Bich S Mädler K Chiesa F DeGiacomo N Bogliotti R Zenobi 2010 Reactivity and applications of new amine reactive cross-linkers for mass spectrometric detection of protein-protein complexes Anal. Chem. 82 172 179 10.1021/ac901651r 1:CAS:528:DC%2BD1MXhsFaisrrF
35. A Svatos R Shroff 2009 Proton sponge: A novel and versatile MALDI matrix for the analysis of metabolites using mass spectrometry Anal. Chem. 81 7954 7959 10.1021/ac901048z
36. F Kirpekar E Nordhoff K Kristiansen P Roepstorff A Lezius S Hahner M Karas F Hillenkamp 1994 Matrix-assisted laser-desorption ionization mass spectrometry of enzymatically synthesized RNA up to 150 kDa Nucleic Acids Res. 22 3866 3870 10.1093/nar/22.19.3866 1:CAS:528:DyaK2MXhslegs7c%3D (Pubitemid 24310095)
37. CF Xu Y Lu J Ma M Mohammadi TA Neubert 2005 Identification of phosphopeptides by MALDI Q-TOF MS in positive and negative ion modes after methyl esterification Mol. Cell. Proteomics 4 809 818 10.1074/mcp.T400019-MCP200 1:CAS:528:DC%2BD2MXlsV2nsrc%3D (Pubitemid 40873009)
38. J Gao CJ Cassady 2008 Negative ion production from peptides and proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 22 4066 4072 10.1002/rcm.3818 1:CAS:528: DC%2BD1MXnsFOntA%3D%3D
39. IA Kaltashov A Mohimen 2005 Estimates of protein surface areas in solution by electrospray ionization mass spectrometry Anal. Chem. 77 5370 5379 10.1021/ac050511+ 1:CAS:528:DC%2BD2MXls1WqsLo%3D (Pubitemid 41140859)
40. B van Breukelen A Barendregt AJR Heck RHH van den Heuvel 2006 Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra Rapid Commun. Mass Spectrom. 20 2490 2496 10.1002/rcm.2620 (Pubitemid 44258455)
41. R Knochenmuss R Zenobi 2003 MALDI ionization: The role of in-plume processes Chem. Rev. 103 441 452 10.1021/cr0103773 1:CAS:528: DC%2BD38XpsFCnsrc%3D
42. K Breuker R Knochenmuss R Zenobi 1999 Gas-phase basicities of deprotonated matrix-assisted laser desorption/ionization matrix molecules Int. J. Mass Spectrom. 184 25 38 10.1016/S1387-3806(98)14200-8 1:CAS:528: DyaK1MXhvF2rsr4%3D
43. CM Jones M Bernier E Carson KE Colyer R Metz A Pawlow ED Wischow I Webb EJ Andriole JC Poutsma 2007 Gas-phase acidities of the 20 protein amino acids Int. J. Mass Spectrom. 267 54 62 10.1016/j.ijms.2007.02.018 1:CAS:528: DC%2BD2sXhtFShs7fN
44. R Knochenmuss 2006 Ion formation mechanisms in UV-MALDI Analyst 131 966 986 10.1039/b605646f 1:CAS:528:DC%2BD28XosFGmsrY%3D (Pubitemid 44313637)
45. F Zhong S Zhao 1995 A study of factors influencing the formation of singly charged oligomers and multiply charged monomers by matrix-assisted laser desorption/ionization mass spectrometry Rapid Commun. Mass Spectrom. 9 570 572 10.1002/rcm.1290090705 1:CAS:528:DyaK2MXmtlCju7w%3D
46. A Brunelle P Chaurand S Dellanegra Y Lebeyec GB Baptista 1993 Surface secondary-electron and secondary-ion emission induced by large molecular ion impacts Int. J. Mass Spectrom. Ion Process 126 65 73 10.1016/0168-1176(93)80071- L 1:CAS:528:DyaK3sXmtFGhu7k%3D
47. RJ Beuhler L Friedman 1980 Threshold studies of secondary electron emission induced by macro-ion impact on solid surfaces Nucl. Instrum. Meth. 170 309 315 10.1016/0029-554X(80)91031-9 1:CAS:528:DyaL3cXktFOlt7o%3D
48. S Coeck M Beck B DelaurÈ VV Golovko M Herbane A Lindroth S Kopecky VY Kozlov IS Kraev T Phalet N Severijns 2006 Microchannel plate response to high-intensity ion bunches Nucl. Instrum. Meth. Phy. Res. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 557 516 522 10.1016/j.nima.2005.11.061 1:CAS:528:DC%2BD28XhtVOqsLs%3D (Pubitemid 43151994)
49. DR Tolan B Schuler PT Beernink R Jaenicke 2003 Thermodynamic analysis of the dissociation of the aldolase tetramer substituted at one or both of the subunit interfaces Biol. Chem. 384 1463 1471 10.1515/BC.2003.162 1:CAS:528:DC%2BD3sXpsFCls7k%3D (Pubitemid 37508650)
50. K Lim JX Ho K Keeling GL Gilliland X Ji F Ruker DC Carter 1994 Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV Protein Sci. 3 2233 2244 10.1002/pro.5560031209 1:CAS:528:DyaK2MXjslajtbw%3D
51. VD Hoagland Jr. DC Teller 1969 Influence of substrates on the dissociation of rabbit muscle D-glyceraldehyde 3-phosphate dehydrogenase Biochemistry 8 594 602 10.1021/bi00830a020 1:CAS:528:DyaF1MXptlersw%3D%3D
52. S Mädler M Seitz J Robinson R Zenobi 2010 Does chemical cross-linking with NHS esters reflect the chemical equilibrium of protein-protein noncovalent interactions in solution? J. Am. Soc. Mass Spectrom. 21 1775 1783 10.1016/j.jasms.2010.06.016