Techniques for high-throughput characterization of peptides, oligonucleotides and catalysis efficiency

Current Opinion in Chemical Biology

Volumn 8, Issue 3, 2004, Pages 327-333

  Kenseth, Jeremy R ^a   He, Yan ^a   Tallman, Dennis ^a   Pang, Ho Ming ^a   Coldiron, Shelley J ^a  

^a CombiSep Inc ^*  (United States)

Author keywords

7 amino 4 carbamoylmethyl coumarin; ACC; capillary gel electrophoresis; CCD; CGE; charge coupled device; electrospray ionization; ESI; focal plane array; FPA; ionization potential; IP; MALDI; matrix assisted laser desorption ionization; PAGE

Indexed keywords

OLIGONUCLEOTIDE; PEPTIDE DERIVATIVE;

ANALYTIC METHOD; CAPILLARY ELECTROPHORESIS; CATALYSIS; COLORIMETRY; COMBINATORIAL CHEMISTRY; DNA SEQUENCE; ELECTROSPRAY MASS SPECTROMETRY; GAS CHROMATOGRAPHY; GEL ELECTROPHORESIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HIGH THROUGHPUT SCREENING; HYDROPHOBICITY; INFRARED PHOTOGRAPHY; INFRARED SPECTROSCOPY; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; PEPTIDE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SITE DIRECTED MUTAGENESIS; TIME OF FLIGHT MASS SPECTROMETRY;

CATALYSIS; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; ELECTROPHORESIS, CAPILLARY; MASS SPECTROMETRY; MATERIALS TESTING; OLIGONUCLEOTIDES; OPTICS; PEPTIDES;

EID: 2942623766     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2004.03.001     Document Type: Review

References (49)

1. Schrader M., Schulz-Knappe P. Peptidomics technologies for human body fluids. Trends Biotechnol. 19:2001;S55-S60
2. Clynen E., Loof A.D., Schoofs L. The use of peptidomics in endocrine research. Gen Comp Endocrinol. 132:2003;1-9
3. Baggerman G, Verleyen P, Clynen E, Huybrechts J, Loof AD, Schoofs L: Peptidomics. J Chromatrogr B 2004, in press.
4. Chernokalskaya E, Kavonian M, Glazebrook H, Gutierrez S, Pitt AM, Leonard J: Parallel purification of serum peptides for mass spectrometry. Millipore Corporation: Application Note 2003. (See http://www.millipore.com/publications. nsf/docs/5RFGVC)
5. Skold K., Svensson M., Kaplan A., Bjorkesten L., Astrom J., Andren P.E. A neuroproteomic approach to targeting neuropeptides in the brain. Proteomics. 2:2002;447-454
6. Heine G., Zucht H-D., Schuhmann M.U., Burger K., Jurgens M., Zumkeller M., Scheekloth C.G., Hampel H., Schulz-Knappe P., Selle H. High-resolution peptide mapping of cerebrospinal fluid: a novel concept for diagnosis and research in central nervous system diseases. J Chromatrogr B. 782:2002;353-361 The authors developed a new technology referred to as differential peptide display (DPD), in which peptides are extracted from biological samples and analyzed by a combination of chromatography and mass spectrometry. Multi-dimensional mass fingerprints used to compare healthy and diseased patients showed obvious differences, representing a new approach for disease diagnosis and therapeutic monitoring.
7. Albert T., Lange S., Oldenburg J., Graw J., Schramm W., Hanfland P., Brackmann H., Schwaab R. Characterization of factor VIII antibody epitopes from hemophilia A patients using cellulose bound FVIII peptide libraries. Hamostaseologie. 23:2003;13-17
8. Mullaney B.P., Pallavicini M.G., Marks J.D. Epitope mapping of neutralizing botulinium neurotoxin A antibodies by phage display. Infect Immun. 69:2001;6511-6514
9. Salisbury C.M., Maly D.J., Ellman J.A. Peptide microarrays for the determination of protease substrate specificity. J Am Chem Soc. 124:2002;14868-14870
10. Gobom J., Schuerenberg M., Mueller M., Theiss D., Lehradch H., Nordhoff E. α-Cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal Chem. 73:2001;434-438
11. Fontoulakis M., Schlaeger E. The mitochondrial proteins of the neuroblastoma cell line IMR-32. Electrophoresis. 24:2003;260-275
12. He Y., Zhong W., Yeung E.S. Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping. J Chromatrogr B. 782:2002;331-341 The authors investigated the application of multiplexed capillary electrophoresis for on-column protein digestion and peptide mapping. Orthogonal peptide maps were generated simultaneously in different capillaries to uniquely identify protein variants. On-column protein digestion resulted in the consumption of only nanoliters of reagents.
13. Tabb D.L., McDonald W.H., Yates J.R. DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res. 1:2002;21-26
14. Lowery J.D., Ugozzoli L., Wallace R.B. Application of capillary electrophoresis to the measurement of oligonucleotide concentration and purity over a wide dynamic range. Anal Biochem. 254:1997;236-239
15. Chen D., Yan Z., Cole D.L., Srivatsa G.S. Analysis of internal (n-1) deletion sequences in synthetic oligodeoxyribonucleotides by hybridization to an immobilized probe array. Nucleic Acids Res. 27:1999;389-395
16. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J: Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 2002, 30:e51-e51(51).
17. Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, Prokhorova A, Gieser L, Touma E, Lockner R, Tata M: An assessment of Motorola CodeLink™ microarray performance for gene expression profiling applications. Nucleic Acids Res 2002, 30:e30-e30(31).
18. Gilar M., Bouvier E.S.P. Purification of crude DNA oligonucleotides by solid-phase extraction and reversed-phase high-performance liquid chromatography. J Chromatogr A. 890:2000;167-177
19. Pippen D: Breaking the bottleneck in oligonucleotide purification. American Genomic/Proteomic Technology 2002, February 2002: http://www.iscpubs. com
20. Behlke M, Tao W: MALDI-TOF mass spectrometry. Integrated DNA Technologies: Technical Bulletin 2000: www.idtdna.com
21. Packman L. MALDI-TOFMS as a rapid quality control method in oligonucleotide synthesis. Anal Biochem. 246:1997;185-194
22. Langley G.J., Herniman J.M., Davies N.L., Brown T. Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 13:1999;1717-1723
23. Bellis G.D., Salani G., Battaglia C., Pietta P., Rosti E., Mauri P. Electrospray ionization mass spectrometry of synthetic oligonucleotides using 2-propanol and spermidine. Rapid Commun Mass Spectrom. 14:2000;243-249
24. Hail M.E., Elliott B., Anderson K. High-throughput analysis of oligonucleotides using automated electrospray ionization mass spectrometry. Am Biotechnol Lab. 22:2004;12-14 An integrated LC/ESI/MS system that incorporates sample desalting before MS analysis is described. Highly accurate mass analysis of oligonucleotides up to 120mer in length can be obtained at a throughput of 1000 samples/day.
25. Dinther F.H.Mv., Bally R.W., Sommeren T.P.Gv. Evaluation of three commercially available capillary (gel) electrophoresis kits for single stranded DNA oligonucleotide analysis. J Chromatogr A. 817:1998;273-279
26. Mangano M.F., Battaglia C., Salani G., Bernardi L.R., Bellis G.D. Composition dependent separation of oligonucleotides by capillary electrophoresis in acidic buffers with application to the quality control of synthetic oligonucleotides. J Chromatogr A. 848:1999;435-442
27. Wei W: High throughput synthetic oligonucleotide analysis with the MCE 2000™ system. CombiSep, Inc: Application Note 2002: www.combisep.com An approach utilizing multiplexed capillary electrophoresis with UV absorbance detection is described that can increase the analytical throughput of oligonucleotide purity analysis more than 20-fold over existing approaches without a sacrifice in data quality.
28. Williams W.A., Hendrickson A., Gillaspy A.F., Dyer D.W., Lewis L.A. Oligonucleotide analysis by sequential injection before analysis (SIBA) capillary electrophoresis. Anal Biochem. 313:2003;183-185
29. Brocke A.V., Freudemann T., Bayer E. Performance of capillary gel electrophoretic analysis of oligonucleotides coupled on-line with electrospray mass spectrometry. J Chromatogr A. 991:2003;129-141 The authors present an integrated CGE-MS system for the comprehensive analysis of both oligonucleotide purity and mass identity.
30. Menger F.M. Phosphatase catalysis developed via combinatorial organic chemistry. J Org Chem. 60:1995;6666-6667
31. Lue ND: Combinatorial chemistry moves beyond pharmaceuticals. Chemical Innovation 2001, November:33-39.
32. Wennemers H. Combinatorial chemistry: a tool for the discovery of new catalysts. Comb Chem High Throughput Screen. 4:2001;273-285
33. Claus P., Honicke D., Zech T. Miniaturization of screening devices for the combinatorial development of heterogenous catalysts. Catal Today. 67:2001;319-339
34. Nayar A., Liu R., Allen R.J., McCall M.J., Willis R.R., Smotkin E.S. Laser-activated membrane introduction mass spectrometry for high-throughput evaluation of bulk heterogenous catalysts. Anal Chem. 74:2002;1933-1938
35. Reetz M.T., Kuhling K.M., Wilensek S., Husmann H., Hausig U.W., Hermes M. A GC-based method for high-throughput screening of enantioselective catalysts. Catal Today. 67:2001;389-396
36. Zhang Y., Gong X., Zhang H., Larock R.C., Yeung E.S. Combinatorial screening of homogenous catalysis and reaction optimization based on multiplexed capillary electrophoresis. J Comb Chem. 2:2000;450-452
37. Potyrailo R.A., Lemmon J.P., Leib T.K. High-throughput screening of selectivity of melt polymerization catalysts using fluorescence spectroscopy and two-wavelength fluorescence imaging. Anal Chem. 75:2003;4676-4681
38. Senkan S., Ozturk S., Krantz K., Onal I. Photoionization detection (PID) as a high throughput screening tool in catalysis. Appl Catal, A. 254:2003;97-106
39. Johann T., Brenner A., Schwickardi M., Busch O., Marlow F., Schunk S., Schuth F. Listening to catalysis - a real time parallel method for high throughput product analysis. Catal Today. 81:2003;449-455
40. Wilkin O.M., Maitlis P.M., Haynes A., Turner M.L. Mid-IR spectroscopy for rapid on-line analysis in heterogenous catalyst testing. Catal Today. 81:2003;309-317
41. Leugers A., Neithamer D.R., Sun L.S., Hetzner J.E., Hilty S., Hong S., Krause M., Beyerlein K. High-throughput analysis in catalysis research using novel approaches to transmission infrared spectroscopy. J Comb Chem. 5:2003;238-244
42. Snively C.M., Oskarsdottir G., Lauterbach J. Chemically sensitive parallel analysis of combinatorial catalyst libraries. Catal Today. 67:2001;357-368
43. Schuth F., Busch O., Hoffmann C., Johann T., Kiener C., Demuth D., Klein J., Schunk S., Strehlau W., Zech T. High-throughput experimentation in oxidation catalysis. Top Catal. 21:2002;55-66
44. Klein J., Stichert W., Strehlau W., Brenner A., Demuth D., Schunk S.A., Hibst H., Storck S. Accelerating lead discovery via advanced screening methodologies. Catal Today. 81:2003;329-335 The authors describe an intelligent combination of complementary analytical techniques for primary screening of catalysts. Non-specific, parallel infrared thermography is used to initially identify active candidates, while chemically informative, lower-throughput mass spectrometry collects reaction information on only the active sites.
45. Su H., Hou Y., Houk R.S., Schrader G.L., Yeung E.S. Combinatorial screening of heterogenous catalysts in selective oxidation of naphthalene by laser-induced fluorescence imaging. Anal Chem. 73:2001;4434-4440
46. Bergh S, Guan S, Hagemeyer A, Lugamair C, Turner H, Jr. AFV, Weinberg WH, Mott G: Gas phase oxidation of ethane to acetic acid using high-throughput screening in a massively parallel microfluidic reactor system. Appl Catal, A 2003, 254:67-76.
47. Garbacia S, Touzani R, Lavastre O: Image analysis as a quantitative screening test in combinatorial catalysis: discovery of an unexpected ruthenium-based catalyst for the Sonogashira reaction. J Comb Chem 2004, 6: in press.
48. Duff D.G., Ohrenberg A., Voelkening S., Boll M. A screening workflow for synthesis and testing of 10, 000 heterogeneous catalysts per day - lessons learned. Macromol Rapid Commun. 25:2004;169-177
49. Peil K.P., Neithamer D.R., Patrick D.W., Wilson B.E., Tucker C.J. Applications of high throughput research at the Dow Chemical Company. Macromol Rapid Common. 25:2004;119-125