Supplementary Information
Absorption-Mode Fourier Transform Mass
Spectrometry: the Effects of Apodization and
Phasing on Modified Protein Spectra
Yulin Qi,1 Huilin Li,1 Rebecca H. Wills,1 Pilar Perez-Hurtado,1 Xiang Yu,2,3 David. P. A. Kilgour,1
Mark P. Barrow,1 and Cheng Lin,2,3 Peter B. O’Connor1
1
Department of Chemistry, University of Warwick, Coventry, United Kingdom, CV4 7AL
2
Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA
02118 USA
3
Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
* Correspondence to: Peter B. O’Connor; E-mail: p.oconnor@warwick.ac.uk
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Figure S1. Transient, window function and its corresponding peak shape by simulation.
A: original transient of a crude oil sample; B to E: full hanning window, apodized transient, and its
corresponding peak shape in the absorption and magnitude-mode; F to I: half hanning window,
apodized transient, and its peak shape in the absorption and magnitude-mode. N is the total number
of data points and n is the index of each data point 0≤n≤N. The figure was partially reprinted with
permission from Ref.13. Copyright (2012) American Chemical Society.
2
Further Discussion on Apodization Functions
The window function affects the relative intensity and S/N in a spectrum, for demonstration, the
crude oil dataset from previous paper1 was re-plotted here. As is seen in Fig.S2A-I, the spectral
intensity (using the same vertical scale) varies by applying different apodization functions: the fullwindow suppresses the signal at both the beginning and the end of the transient, while a half-window
retains the intense part at the beginning. Furthermore, it should be pointed out that the full window
function generates large negative intensities in the absorption-mode (Fig.S2I), an interesting
phenomenon which was first reported by Comisarow et al. 24 years ago,2 and is largely dependent
on the density of peaks in the spectrum. For further study, narrow m/z windows in both low and
high m/z regions were expanded to compare the peak shape results from different window functions.
As is shown in Fig.S3, both half and full windows smooth the peak shape compared to unapodized
spectra, and the full window will have a narrower peak width than the half one. Additionally, the
full window leads to large negative intensities in absorption-mode, and thus, distorts the peak shape.
In the low m/z region, when the peaks are well resolved, Fig.S3C shows a typical absorption-mode
peak shape from full window function. Meanwhile, when the peaks become dense in the high m/z
region, the negative sidebands will interact with peaks nearby causing severe spectral distortion
(Fig.S3F). In conclusion, the full window apodization has a narrower peak width compared to the
half window (Fig.S1E&I), and thus is recommended in the magnitude-mode spectrum for better
resolving power and peak shape, but the half window function is preferred in absorption-mode for
better peak shape and S/N.
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Figure S2. (A-C): Transient (black) and m/z spectra in magnitude- (blue) and absorption-mode (red)
without apodization. (D-F): Transient and spectra with a half Hanning window apodization. (G-I):
Transient and spectra with a full Hanning window apodization.
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Figure S3. Close-up of two narrow m/z windows from Fig. S2, in both magnitude (blue) and
absorption-mode (red). (A-C): m/z 277.099−277.107 with no apodization, half Hanning, and full
Hanning apodization. (D-F): m/z 751.55−751.75 with no apodization, half Hanning, and full
Hanning apodization.
Reference
1. Qi, Y.,Barrow, M. P.,Li, H.,Meier, J. E.,Van Orden, S. L.,Thompson, C. J.,O'Connor, P. B.:
Absorption-Mode: The Next Generation of Fourier Transform Mass Spectra. Anal. Chem., 84, 29232929 (2012)
2. Lee, J. P.,Comisarow, M. B.: Advantageous Apodization Functions for Absorption-Mode Fourier
Transform Spectroscopy. Appl. Spectrosc., 43, 599-604 (1989)
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