Developments in matrix-assisted laser desorption/ionization peptide mass spectrometry

Current Opinion in Biotechnology

Volumn 7, Issue 1, 1996, Pages 11-19

  Mann, Matthias ^a   Talbo, Gert ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

AMINO ACID SEQUENCE; ANALYTIC METHOD; IONIZATION; LASER; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; REVIEW;

EID: 0030041205     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(96)80089-9     Document Type: Article

References (74)

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7. Johnson RE: Models for matrix-assisted desorption by a laser pulse. Int J Mass Spectrom Ion Process 1994, 139:25-28. Presents a comparison of different models suggested for the desorption event.
8. •]). The authors find that the experimental results given here favor a quasi-thermal desorption model.
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10. Beavis RC, Chaudhary T, Chait BT: α-Cyano-4-hydroxycinnamic acid as a matrix for matrix assisted laser desorption mass spectrometry. Org Mass Spectrom 1992, 27:156-158.
11. •].
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13. Gusev AI, Wilkinson WR, Proctor A, Hercules DM: Improvement of signal reproducibility and matrix/comatrix effects in MALDI analysis. Anal Chem 1995, 67:1034-1041.
14. Xiang F, Beavis RC: A method to increase contaminant tolerance in protein matrix-assisted laser desorption/ionization by the fabrication of thin protein-doped polycrystalline films. Rapid Comm Mass Spectrom 1994, 8:199-204. In this method, a drop of matrix solution is dried on the probe tip and the deposit crushed by a glass slide. Protein from a protein/matrix solution is then included into matrix crystals at the 'seed sites', before substantial evaporation has occurred. The method yields analyte ion signal from glycerol and other contamination-containing solutions. Other advantages of the method are increased 'washability' and uniformity of sample surfaces.
15. Beavis RC, Chait BT: Matrix-assisted laser desorption mass spectrometry of proteins. Methods Enzymol 1996, in press.
16. Jensen ON, Shevchenko A, Mann M: Protein analysis by mass spectrometry. In Protein Structure-A Practical Approach, edn 2. Edited by Creighton TE. Oxford: Oxford University Press; 1696:in press.
17. Vorm O, Roepstorff P, Mann M: Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal Chem 1994, 66:3281-3287. Matrix matrial is dissolved in a fast-evaporating solvent, such as acetone, and deposited on the probe tip to form a homogenous surface just -5 μm in thickness. Peptide solution is subsequently applied and allowed to dry. These surfaces permit resolution of > 5000, attomole sensitivity and higher sequence coverage in peptide mixtures.
18. Nicola AJ, Gusev AI, Proctor A, Jackson EK, Hercules DM: Application of the fast-evaporation sample preparation method for Improving quantification of angiotensin II by matrix-assisted laser desorption/ionization. Rapid Comm Mass Spectrom 1995, 9:1164-1171.
19. Strupat K, Karas M, Hillenkamp F, Eckerskorn C, Lottspeich F: Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide gel electrophoresis. Anal Chem 1994, 66:464-470. Reports these authors' continuing work aimed at obtaining the intact molecular weight of proteins separated on polyacrylamide gels. Proteins are electroblotted, the membranes are incubated with matrix material and MALDI with infrared lasers is performed. Different membranes and stains are investigated.
20. Vestling MM, Fenselau C: Poly(vinylidene difluoride) membranes as the interface between laser desorption mass spectrometry, gel electrophoresis and in situ proteolysis. Anal Chem 1994, 66:471-477.
21. Bai J, Liu Y-H, Cain TC, Lubman DM: Matrix-assisted laser desorption/ionization using an active perfluorosulfonated lonomer film substrate. Anal Chem 1994, 66:3423-3430.
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23. •].
24. Hutchens TW, Yip TT: New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Comm Mass Spectrom 1993, 7:576-780.
25. Dogruel D, Williams P, Nelson RW: Rapid tryptic mapping using enzymatically-active mass spectrometer probe tips. Anal Chem 1995, 67:4343-4346. In this report, enzyme is immobilized directly on the probe tip. A mass spectrometric peptide map is obtained within minutes of depositing the protein solution on the tip. The advantages of the procedure are reduced digestion time, absence of autolysis products and minimization of irreversible adsorption of the generated peptides.
26. Juhasz P, Biemann K: Mass spectrometric molecular-weight determination of highly acidic compounds of biological significance via their complexes with basic polypeptides. Proc Natl Acad Sci USA 1994, 91:4333-4337. Highly negatively charged compounds are found difficult or impossible to ionize. By mixing them with highly positively charged molecules (arginine-containing peptides), these authors are able to determine the molecular weight of the resultant complex bound by electrostatic forces.
27. •].
28. •] provide excellent guidelines for the combination of high-sensitivity 'internal' protein sequencing with MALDI. This chapter discusses the various pitfalls and gives practical tips. It also describes the sampling of the lymph of honeybees for direct MALDI analysis.
29. Vorm O, Mann M: Improved mass accuracy in matrix assisted laser desorption/ionization time-of-flight mass spectrometry of peptides. J Am Soc Mass Spectrom 1994, 5:955-958. First demonstration that MALDI can be a highly accurate mass measurement technique. The 'fast evaporation surfaces' allow use of the matrix ions as internal calibrants in a spectrum. Better than 50 ppm mass accuracy is demonstrated in peptide mixtures. In a favorable case (i.e. analysis of the degradation products of an isolated model peptide), an average mass accuracy of 12 ppm was obtained.
30. •]).
31. •].
32. •] investigate 'delayed extraction' as a means to obtain high resolution in linear mass spectrometers. The extraction field is applied a short time after the laser pulse so that ions can be extracted some distance from the probe tip, instead of from the dense region created by the laser shot. This technique is highly promising because it offers high performance in relatively simple instruments. It may also reduce fragmentation of analyte ions. Mass calibration over a wide mass range, especially external calibration, is not addressed in these papers.
33. r=5733.5) should put to rest the notion that MALDI TOF is necessarily a tow-resolution technique. Unfortunately, the paper makes no mention of the mass accuracies obtained.
34. Chait BT, Wang R, Beavis RC, Kent S: Protein ladder sequencing. Science 1993, 262:89-92.
35. Bartet-Jones M, Jeffery WA, Hansen HF, Pappin DJC: Peptide ladder sequencing by mass spectrometry using a novel, volatile degradation reagent. Rapid Comm Mass Spectrom 1994, 8:737-742. By adding a volatile Edman reagent in each step (together with a portion of the peptide solution), a peptide ladder is obtained. Use of volatile reagents should mean less sample handling and less extractive losses.
36. Thiede B, Wittmann-Liebold B, Biernert M, Krause E: MALDI-MS for C-terminal sequence determination of peptides and proteins degraded by carboxypeptidase Y and P. FEBS Lett 1995, 357:65-69.
37. Wood AS, Huang AYC, Cotter RJ, Pastemack GR, Pardoll DM, Jaffee EM: Simplified high-sensitivity sequencing of a major histocompatibility complex class I-associated immunoreactive peptide using matrix-assisted laser desorption/ionization mass spectrometry. Anal Biochem 1995, 226:15-25.
38. Vorm O, Roepstorff P: Peptide sequence information derived by partial acid hydrolysis and matrix-assisted laser desorption/ionization mass spectrometry. Biol Mass Spectrom 1994, 23:734-740.
39. Knierman MD, Coligan JE, Parker KC: Peptide fingerprints after partial acid hydrolysis: analysis by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Comm Mass Spectrom 1994, 8:1007-1010.
40. Machold J, Ulkin Y, Kirsch D, Kaufmann R, Tsetlin V: Photolabeling reveals the proximity of the a-neurotoxin binding site to the M2 helix of the ion channel in the nicotinic acetylcholine receptor. Proc Natl Acad Sci USA 1995, 92:7282-7286. One of the first biologically significant applications of sequencing by PSD. The location of a pholoaffinity label is determined by PSD. In addition, the authors develop various aids in sequence interpretation of PSD spectra.
41. Kellner R, Talbo G, Houthaeve T, Mann M: Edman degradation and MALDI sequencing enables N- and C-terminal sequence analysis of peptides. In Techniques in Protein Chemistry VI. Edited by Crabb JW. New York: Academic Press; 1995:47-54. Partial sequence information obtained by PSD is combined with ambiguous Edman degradation data to yield complete and accurate sequences.
42. Nelson RW, McLean MA, Hutchens TW: Quantitative determination of proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 1994, 66:1408-1415.
43. Jespersen S, Niessen WMA, Tjaden UR, Van der Greef J: Quantitative bioanalysis using matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 1995, 30:357-364.
44. Kanda F, Yoshida S, Okumura T, Takamatsu T: Asparaginyl endopeptidase mapping of proteins with subsequent matrix-assisted laser desorption/ionization mass spectrometry. Rapid Comm Mass Spectrom 1995, 9:1095-1100.
45. Andersen JS, Søgaard M, Svensson B, Roepstorff P: Localization of an O-glycosylated site in the recombinant barley α-amylase 1 produced in yeast and correction of the amino acid sequence using matrix-assisted laser desorption/ionization mass spectrometry of peptide mixtures. Biol Mass Spectrom 1994, 23:547-554.
46. Patterson SD: Matrix-assisted laser desorption/ionization mass spectrometric approaches for the Identification of gel-separated proteins in the 5-50 pmol range. Electrophoresis 1995, 16:1104-1114.
47. Rasmussen HH, Mørtz E, Mann M, Roepstorff P, Celis JE: Identification of transformation sensitive proteins recorded in human two-dimensional gel protein databases by mass spectrometric peptide mapping alone and in combination with microsequencing. Electrophoresis 1994, 15:406-413.
48. Clauser KR, Hall SC, Smith DM, Webb JW, Andrews LE, Tran HM, Epstein LB, Burlingame AL: Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. Proc Natl Acad Sci USA 1995, 92:5072-5076.
49. Cordwell SJ, Wilkins MR, Cerpa-Poljak A, Gooley AA, Duncan M, Williams KL, Humphery-Smith I: Cross-species identification of proteins separated by two-dimensional gel electrophoresis using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and amino acid composition. Electrophoresis 1995, 16:438-443. An interesting approach to database identification of proteins is presented. Identification by laser desorption mass spectrometry alone is found to be unreliable, and the same holds true for amino acid analysis. Combining results from the two techniques, however, meets with some success, and - according to these authors - it can even be used to identify highly homologous proteins across species boundaries.
50. Liao P-C, Leykam J, Andrews PC, Gage DA, Allison J: An approach to locate phosphorylatlon sites in a phosphoprotein: mass mapping by combining specific enzymatic degradation with matrix-assisted laser desorption/ionization mass spectrometry. Anal Biochem 1994, 219:9-20. Practical protocols are developed for identifying phosphorylation sites by comparison of MALDI peptide maps before and after phosphalase treatment.
51. Zhang W, Czernik AJ, Youngwirth T, Aebersold R, Chait B: Matrix-assisted laser desorption mass spectrometric peptide mapping of proteins separated by two-dimensional gel electrophoresis: determination of phosphorylation in synapsin I. Protein Sci 1995, 3:677-686.
52. Patterson SD, Katta V: Prompt fragmentation of disulfide-linked peptides during matrix-assisted laser desorption ionization mass spectrometry. Anal Chem 1994, 66:3727-3732.
53. Crimmins DL, Saylor M, Rush J, Thoma RS: Facile, in situ matrix-assisted laser desorption ionization-mass spectrometry analysis and assignment of disulfide pairings in heteropeptide molecules. Anal Biochem 1995, 226:355-361.
54. Huberty MC, Vath JE, Yu W, Martin SA: Site-specific carbohydrate identification in recombinant proteins using MALD-TOF MS. Anal Chem 1993, 65:2791-2800.
55. Talbo G, Mann M: Distinction between phosporylated and sulfated peptides by matrix assisted laser desorption ionization reflector mass spectrometry at the sub picomole level. In Techniques in Protein Chemistry V. Edited by Crabb JW. New York: Academic Press; 1994:105-113. The fragmentation behavior of model phosphorylated and sulfated peptides in PSD is studied. After fragmentation, phosphorylated peptides yield a unique marker ion 98 Da below the parent ion mass (arising because of loss of the phospho group). Sulfated peptides, which share a mass addition +80 Da to the unmodified peptide sequence, can be distinguished by their different fragmentation behavior. These differences are exploited to distinguish between phosphorylated and sulfated peptides.
56. Darby NJ, Morin PE, Talbo G, Chreighton TE: Refolding of bovine pancreatic trypsin inhibitor via non-native disulphide intermediates. J Mol Biol 1995, 249:463-477.
57. Nakanishi T, Okamoto N, Tanaka K, Shimizu A: Laser desorption time-of-flight mass spectrometric analysis of transferrin precipitated with antiserum: a unique simple method to identify molecular weight variants. Biol Mass Spectrom 1994, 23:230-233. Transferrin is immunoprecipitated out of serum and the precipitate loaded onto a target. Different molecular weight species are measured. This one-step preparation method is simple and should find wide application.
58. Nelson RW, Krone JR, Bieber AL, Williams P: Mass spectrometric immunoassay. Anal Chem 1995, 67:1153-1158. A general method to measure the mass of antigens by MALDI is developed. An antigen with a different molecular weight serves as an internal standard for quantification. Subnanomolar concentration sensitivities are demonstrated in human blood and reasonable resolution is achieved.
59. Zhao Y, Chait BT; Protein epitope mapping by mass spectrometry. Anal Chem 1994, 66:3723-2726. Peptide mixtures obtained from proteolytic digestion of an antigen are immunoprecipitated by an antibody. The bound peptides are released and analyzed by MALDI. A comparison of the results of several proteolytic digestions allows definition of the epitope to within one or a few residues.
60. Papac DI, Hoyes J, Tomer KB: Direct analysis of affinity-bound analytes by MALDI/TOF MS. Anal Chem 1994, 66:2609-2613. Antigens bound to antibody-covered beads are analyzed by MALDI either directly or after previous separation of antigen into the supernatant. Metal-binding proteins and phosphorylated peptides are also analyzed directly after binding to immobilized metal ion affinity beads.
61. Papac DI, Hoyes J, Tomer KB: Epitope mapping of the gastrin-releasing peptide/anti-bombesin monoclonal antibody complex by proteolysis followed by matrix-assisted laser desorption ionization mass spectrometry. Protein Sci 1994, 3:1485-1492.
62. Cohen SL, Ferre-D'Amare AR, Burley SK, Chait BT: Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci 1995, 4:1088-1099. A protein-DNA complex is digested by proteolytic enzymes and the resulting peptides analyzed by MALDI. A comparison of the results obtained after digestion of the complex and of the protein alone by different enzymes allows determination of the sites in the protein that are protected from digestion by contact to DNA.
63. Bennett SE, Jensen ON, Barofsky DF, Mosbaugh DW: UV-catalyzed cross-linking of Escherichia coli uracil-DNA glycosylase to DNA: Identification of amino acid residues In the single stranded DNA binding site. J Biol Chem 1994, 269:21870-21879. A protein-DNA complex is photochemically crosslinked and digested by a proteolytic enzyme. Identification of the DNA - peptide pieces after high-pressure liquid chromatography (HPLC) allows definition of the DNA-protein interaction region.
64. Youngquist RS, Fuentes GR, Lacey MP, Keough T: Matrix-assisted laser desorption ionization for rapid determination of the sequences of biologically active peptides Isolated from support-bound combinatorial peptide libraries. Rapid Comm Mass Spectrom 1994, 8:77-81. A peptide library is synthesized using a solution of amino acids containing 10% acetyl-D,L-alanine. This generates a series of truncated peptides in addition to the full-length ones. The MALDI read-out from a peptide bound to a selected bead immediately reveals the sequence. The method is applied to a model case of epitope mapping.
65. Jiminez CR, Van Veelen PA, Li KW, Wildering WC, Geraerts PM, Tjaden UR, Van der Greet J: Neuropeptide expression and processing as revealed by direct matrix-assisted laser desorption ionization mass spectrometry of single neurons. J Neurochem 1994, 62:404-407. In this and other publications, these authors demonstrate that MALDI can be used for the analysis of unpurified biological material, in this case, a giant single cell. The major peptide components of the cell are obtained, revealing information about peptide processing.
66. Jespersen S, Niessen WM, Tjaden UR, Greef JVD, Litbom E, Lindberg U, Roeraade J: Attomole detection of proteins by matrix-assisted laser desorption/ionization mass spectrometry with the use of picoliter vials. Rapid Comm Mass Spectrom 1994, 8:581-584. Model protein and matrix solutions are filled into etched depressions on chip surfaces ('vials'). These vials are then irradiated by laser pulses, producing MALDI spectra from minimal amounts of protein.
67. Robert T, McIver J, Li Y, Hunter RL: High-resolution laser desorption mass spectrometry of peptides and small proteins. Proc Natl Acad Sci USA 1994, 91:4801-4805. Mass resolution of more than one million is demonstrated for a MALDI/FTMS combination.
68. Pasa-Tolic L, Huang Y, Guan S, Kim HS, Marshall AG: Ultrahigh-reslution matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectra of peptides. J Mass Spectrom 1995, 30:825-833.
69. Wu J, Fannin ST, Franklin WA, Molinski TF, Lebrilla CB: Exact mass determination for elemental analysis of ions produced by matrix-assisted laser desorption. Anal Chem 1995, 67:3788-3792. One of the first times that the potentially powerful technique of MALDI/FTMS has been used to measure the mass of unknown samples. Repeated measurements on two peptides employing internal standards yielded a mass accuracy of 3 ppm.
70. Castoro JA, Wilkins CL, Wood AS, Cotter RJ: Peptide amino acid sequence analysis using matrix-assisted laser desorption/ionization and Fourier transform mass spectrometry. J Mass Spectrom 1995, 30:94-98.
71. Huang Y, Pasa-Tolic L, Guan S, Marshall AG: Collision-induced dissociation for mass spectrometric analysis of biopolymers: high-resolution Fourier transform ion cyclotron resonance MS Anal Chem 1994, 66:4385-4389.
72. Doroshenko VM, Cotter RJ: High-performance collision-induced dissociation of peptide ions formed by matrix-assisted laser desorption/ionization in a quadrupole ion trap mass spectrometer. Anal Chem 1995, 67:2180-2167.
73. Qin J, Chait B: Preferential fragmentation of protonated gas-phase peptide ions adjacent to acidic residues. J Am Chem Soc 1995, 117:5411-5412. The authors have constructed a very promising MALDI/quadrupole ion trap combination. Single laser shots are sufficient to fill the ion trap. This paper describes the fragmentation that is observed directly upon trapping the MALDI-produced ions in the ion trap.
74. Lee H, Lubman DM: Sequence-specific fragmentation generated by matrix-assisted laser desorption/ionization in a quadrupole ion trap/reflectron time-of-flight device. Anal Chem 1995, 67:1400-1408. This paper describes continuing work on a combination of an ion trap and a TOF analyzer. Ions are captured in a simple quadrupole ion trap and decay after millisecond time periods. They are then ejected into a reflector instrument where the fragments can be mass assigned.