Abstract
Nucleotides are a class of molecules that play an essential role in biological systems. A new method has been developed in the detection of nucleotides. These molecules can exist as monomers or constituents of oligomers and polymers. As such, they carry from one to several negative charges. In this study, different cationic ion-pairing reagents were used to complex with each of the 28 nucleotide monomers and nucleotide containing compounds. By using this method, this discrete set of anions was able to be detected in the positive-mode electrospray ionization mass spectrometry, as positively charged complexes. Tandem mass spectrometry experiments were also completed on the ion-pairing reagents that performed the best in the single ion monitoring (SIM) ion mode, and the sensitivity was lowered even further for most of the anions. Limits of detection for compounds such as thymidine diphosphate were improved as much as 100 times compared to the positive SIM mode, and 750 times when compared to the negative mode. A few nucleotides did not show a significant increase in sensitivity when analyzed in the positive ion mode, but in general the new method developed herein resulted in a much greater sensitivity than traditional detection in the negative mode.
Similar content being viewed by others
References
Boyer R (2004) Concepts in biochemistry, 3dth edn. Wiley, New York, pp 282–348
Garret, RH, Grisham CM (2005) Biochemistry. 3d Ed. Thomson, Brooks/Cole pp. 541-618
Gomez D, Fernandez JA, Astigarraga E, Marcaide A, Azcarate S (2007) Current Topics in Sol State Phys 4:2185–2189
Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW (2010) Nat Meth 7:461–465
Wampler FM III, Blades AT, Kebarle P (1993) J Am Soc Mass Spectrom 4:289–95
Zhao X, Huan C, Huang C (2010) Trends Anal Chem 29:354–367
Fujii S, Inagaki K, Takatsu A, Yarita T, Chiba K (2009) J Chromatogr A 1216:7488–7492
Singhal P, Kuhr WG (1997) Anal Chem 69:4828–4832
Cashion PJ, Notman HJ, Cadger TB, Sathe GM (1977) Anal Biochem 80:654–655
Huang Z, Petty JT, O'Quinn B, Longmire JL, Brown NC, Jett JH, Keller RA (1996) Nucleic Acids Res 24:4202–4209
Markovits J, Roques BP, Le Pecq JB (1979) Anal Biochem 94:259–264
Standard SA, Vaux P, Bray CM (1985) J Chrom 318:433–439
Childs KF, Ning X, Bolling SB (1996) J Chromatogr B 678:181–186
Carter AJ, Mueller RE (1990) J Chrom 527:31–39
Weng QM, Hammargren WM, Slowikowski D, Schram KH, Borysko KZ, Wotring LL, Townsend LB (1989) Anal Biochem 178:102–106
Soga T, Ueno Y, Naraoka H, Matsuda K, Tomita M, Nishioka T (2002) Anal Chem 74:6224–6229
Feng Y, Zhu J (2006) Anal Chem 78:6608–6613
Mengel-Jorgensen J, Sanchez JJ, Borsting C, Kirpekar F, Morling N (2004) Anal Chem 76:6039–6045
Soukup-Hein RJ, Remsburg JW, Dasgupta PK, Armstrong (2007) Anal Chem 79:7346–7352
Lin X, Gerardi AR, Breitbach ZS, Armstrong DW, Colyer CL (2009) Electrophoresis 30:3918–3925
Remsburg JW, Soukup-Hein RJ, Crank JA, Breitbach ZS, Payagala T, Armstrong DW (2008) J Am Soc Mass Spectrom 19:261–269
Soukup-Hein RJ, Remsburg JW, Breitbach ZS, Sharma PS, Payagala T, Wanigasekara E, Huang J, Armstrong DW (2008) Anal Chem 80:2612–2616
Martinelago PK, Anderson JL, Dasgupta PK, Armstrong DW, Al-Horr RS, Slingsby RW (2005) Anal Chem 77:4829–4835
Warnke MM, Breitbach ZS, Dodbiba E, Wanigasekara E, Zhang X, Sharma PS, Armstrong DW (2008) J Am Soc Mass 20:529–538
Warnke MM, Breitbach ZS, Dodbiba E, Crank JA, Payagala T, Sharma PS, Wanigasekara E, Zhang X, Armstrong DW (2009) Anal Chem Acta 633:232–237
Breitbach ZS, Warnke MM, Wanigasekara E, Zhang X, Armstrong DW (2008) Anal Chem 80:8828–8834
Zhang X, Wanigasekara E, Breitbach ZS, Dodbiba E, Armstrong D (2010) Rap Comm of Mass Spec 24:1113–1123
Cech NB, Enke CG (2001) Mass Spectrom Rev 20:362–387
Kebarle P, Yeunghaw H In Electrospray Ionization Mass Spectrometry; Cole, R.B. Ed. Wiley P: New York, 1997, p.14
Sharma PS, Payagala T, Wanigasekara E, Wijeratne AB, Huang J, Armstrong DW (2008) Chem Mater 20:4182–4184
Payagala T, Huang J, Breitbach ZS, Sharma PS, Armstrong D (2007) Chem Mater 19:5848–5850
Wanigasekara E, Zhang X, Nanayakkara Y, Payagala T, Moon H, Armstrong DW (2009) Chem Mater 1:2126–2133
Isidoros B, Newshalme EA (1975) Biochem J 151:23–32
Acknowledgment
The authors gratefully acknowledge the Robert A. Welch Foundation for its monetary support.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Dodbiba, E., Breitbach, Z.S., Wanigasekara, E. et al. Detection of nucleotides in positive-mode electrospray ionization mass spectrometry using multiply-charged cationic ion-pairing reagents. Anal Bioanal Chem 398, 367–376 (2010). https://doi.org/10.1007/s00216-010-3949-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00216-010-3949-4