Abstract
Fourier transform mass spectrometry (FTMS) of the isolated isotopic distribution for a highly charged biomolecule produces time-domain signal containing large amplitude signal “beats” separated by extended periods of much lower signal magnitude. Signal-to-noise ratio for data sampled between beats is low because of destructive interference of the signals induced by members of the isotopic distribution. Selective blanking of the data between beats has been used to increase spectral signal-to-noise ratio. However, blanking also eliminates signal components and, thus, can potentially distort the resulting FT spectrum. Here, we simulate the time-domain signal from a truncated isotopic distribution for a single charge state of an antibody. Comparison of the FT spectra produced with or without blanking and with or without added noise clearly show that blanking does not improve mass accuracy and introduces spurious peaks at both ends of the isotopic distribution (thereby making it more difficult to identify posttranslational modifications and/or adducts). Although the artifacts are reduced by use of multiple Gaussian (rather than square wave) windowing, blanking appears to offer no advantages for identifying true peaks or for mass measurement.
ᅟ
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Marshall, A.G., Verdun, F.R.: Fourier Transforms in NMR, Optical, and Mass Spectrometry: A User’s Handbook, pp. 460. Elsevier, Amsterdam (1990)
Senko, M.W., Beu, S.C., McLafferty, F.W.: Automated assignment of charge states from resolved isotopic peaks for multiply charged ions. J. Am. Soc. Mass Spectrom. 6, 52–56 (1995)
Ge, Y., Lawhorn, B.G., EI-Naggar, M., Strauss, E., Park, J.-H., Begley, T.P., McLafferty, F.W.: Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J. Am. Chem. Soc. 124, 672–678 (2002)
Ge, Y., Rybakova, I.N., Xu, Q., Moss, R.L.: Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state. Proc. Natl. Acad. Sci. U. S. A. 106, 12658–12663 (2009)
Lee, J.E., Kellie, J.F., Tran, J.C., Tipton, J.D., Catherman, A.D., Thomas, H.M., Ahlf, D.R., Durbin, K.R., Vellaichamy, A., Ntai, I., Marshall, A.G., Kelleher, N.L.: A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. J. Am. Soc. Mass Spectrom. 20, 2183–2191 (2009)
Valeja, S.G., Kaiser, N.K., Xian, F., Hendrickson, C.L., Rouse, J.C., Marshall, A.G.: Unit mass baseline resolution for an intact 148 kDa therapeutic monoclonal antibody by Fourier fransform ion cyclotron resonance mass spectrometry. Anal. Chem. 83, 8391–8395 (2011)
Wood, T.D., Chen, L.H., Kelleher, N.L., Little, D.P., Kenyon, G.L., McLafferty, F.W.: Direct sequence data from heterogeneous creatine kinase (43 kDa) by high-resolution tandem mass spectrometry. Biochemistry 34, 16251–16254 (1995)
Zhang, H., Cui, W., Wen, J., Blankenship, R.E., Gross, M.L.: Native electrospray and electron-capture dissociation in FTICR mass spectrometry provide top-down sequencing of a protein component in an intact protein assembly. J. Am. Soc. Mass Spectrom. 21, 1966–1968 (2010)
Hofstadler, S.A., Bruce, J.E., Rockwood, A.L., Anderson, G.A., Winger, B.E., Smith, R.D.: Isotopic beat patterns in Fourier transform ion cyclotron resonance mass spectrometry: implications for high resolution mass measurements of large biopolymers. Int. J. Mass Spectrom. Ion Process. 132, 109–127 (1994)
Kelleher, N.L., Senko, M.W., Siegel, M.M., McLafferty, F.W.: Unit resolution mass spectra of 112kDa molecules with 3 Da accuracy. J. Am. Soc. Mass Spectrom. 8, 380--383 (1997)
Muddiman, D.C., Null, A.P., Hannis, J.C.: Precise mass measurement of a double-stranded 500 base-pair (309kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 13, 1201--1204 (1999)
Pasa Tolic, L., Anderson, G.A., Smith, R.D., Brothers II, H.M., Spindler, R., Tomalia, D.A.: Electrospray ionization Fourier transform ion cyclotron resonance mass spectyrometric characterization of high molecular mass Starburst dendrimers. Int. J. Mass Spectrom. Ion Process. 165/166, 405–418 (1997)
Pasa Tolic, L., Bruce, J.E., Paula Lei, Q., Anderson, G.A., Smith, R.D.: In-trap cleanup of proteins from electrospray ionization using soft sustained off-resonance irradiation with Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 70, 405–408 (1998)
Senko, M.W., Guan, S., Huang, Y., Marshall, A.G., McLafferty, F.W.: FT and non-FT Spectral Analysis of Unevenly Sampled Biomolecule ICR Time-Domain Data. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, pp. 806. Atlanta, GA (1995)
Kaiser, N.K., Quinn, J.P., Blakney, G.T., Hendrickson, C.L., Marshall, A.G.: A novel 9.4 tesla FTICR mass spectrometer with improved sensitivity, mass resolution an mass range. J. Am. Soc. Mass Spectrom. 22, 1343–1351 (2011)
Senko, M.W., Hendrickson, C.L., Emmett, M.R., Shi, S.D.-H., Marshall, A.G.: External accumulation of ions for enhanced electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 8, 970–976 (1997)
Blakney, G.T., Hendrickson, C.L., Marshall, A.G.: Predator data station: a fast data acquisition system for advanced FT-ICR MS experiments. Int. J. Mass Spectrom. 306, 246–252 (2011)
Ledford Jr., E.B., Rempel, D.L., Gross, M.L.: Space charge effects in Fourier transform mass spectrometry. Mass malibration. Chem. 56, 2744–2748 (1984)
Shi, S.D.-H., Drader, J.J., Freitas, M.A., Hendrickson, C.L., Marshall, A.G.: Comparison and interconversion of the two most common frequency-to-mass calibration function for Fourier transform ion cyclotron resonance mass spectrometry. Int. J. Mass Spectrom. 195/196, 591–598 (1999)
Verdun, F.R., Giancaspro, C., Marshall, A.G.: Effects of noise, time-domain damping, zero-filling and the FFT algorithm on the “exact interpolation of fast Fourier transform spectra. Appl. Spectrosc. 42, 715–721 (1988)
Guan, S., Li, G.-Z., Marshall, A.G.: Effect of ion-neutral collision mechanism on trapped-ion equation of motion: a new mass spectral line shape for high-mass trapped ions. Int. J. Mass Spectrom. Ion Process. 167/168, 185–194 (1998)
Acknowledgments
The authors thank Jason C. Rouse for providing the antibody sample. This work was supported by the NSF Division of Materials Research through DMR-11-57490 and the State of Florida.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
ESM 1
(DOC 189 kb)
Rights and permissions
About this article
Cite this article
Xian, F., Valeja, S.G., Beu, S.C. et al. Artifacts Induced by Selective Blanking of Time-Domain Data in Fourier Transform Mass Spectrometry. J. Am. Soc. Mass Spectrom. 24, 1722–1726 (2013). https://doi.org/10.1007/s13361-013-0735-5
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13361-013-0735-5