Supplemental Material:

Dynamic Collision-Induced Dissociation (DCID) in a Quadrupole Ion Trap Using a Two-Frequency Excitation Waveform:

II. Effects of frequency spacing and scan rate

Ünige A. Laskay, Olivier L. Collin, Jennifer J. Hyland, Brad Nichol, Glen P. Jackson*

Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701-2979, USA

Sofie P. Pasilis

Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008,

Oak Ridge, TN37831-6131

Douglas C. Duckworth

Pacific Northwest National Laboratory, POB 999, Richland, WA99352USA

Running Title: CID during mass acquisition in a QIT (II)

#Current address Department of Chemistry, University of Illinois, Urbana, Illinois, USA

*Address reprint requests to: Glen P. Jackson, Department of Chemistry and Biochemistry, OhioUniversity, 136 Clippinger Laboratories, Athens, OH45701-2979, USA.

Email:

Tel: 740-593-0797

This section describes the fragmentation studies of the synthetic peptide tetraalanine using dynamic CID (DCID) on a Thermo Electron Polaris Q mass spectrometer modified with an electrospray interface described earlier [1]. Tetraalanine (>99%) purchased from Bachem was dissolved in a 1:1 (v:v) methanol:water mixture containing 0.1% formic acid (Fluka, ~98%) to a 0.45 to 0.48 mM concentration. Spray voltage was typically 4 - 4.5kV; solvent flow rate was set to 3.5 - 4 L/min.The first of the excitation frequencies was held constant at 83 kHz (qz=0.22) and the second frequency was changed in 0.05 kHz increments to 20 kHz. The excitation amplitude was 2.5 Vpp and the relative phase angle of the two excitation frequencies was set to 0° for all experiments. The relative intensities of the precursor ion, the resonantly ejected ions and b3 and y2 product ions at these experimental conditions are shown in Figure 1S. The main product ions of tetraalanine fragmentation are the MH+-H2O ion, the b3, y2, b2, a2 and the de-ammoniated a3 ion [2, 3]. For the purpose of illustrating the DCID efficiencies, the relative intensities of the most abundant ions, the b3 and y2 ions, are monitored. It can be seen in Figure 1S that at frequency spacings above 12 kHz the relative and absolute intensities of the b3 and y2 ions are reasonably constant. Only a small amount of resonance ejection is observed at frequency spacings greater than 12 kHz.

In Figure 2Sa, the excitation waveform consists of two frequencies spaced 1 kHz apart (83 and 84 kHz) and shows very different fragmentation efficiencies depending on the scanning rate, in agreement with results obtained for n-butylbenzene. Under these conditions, even at a threefold reduction of the scanning rate from 0.18 to 0.5 ms/Th the interference pattern of the excitation waveform during on-resonance excitation is crucial; here the time-window of the resonance excitation is not wide enough to overcome the effect of the interference pattern. In contrast, wide frequency spacings reduce this effect even at fast scan rates, as shown in Figure 2Sb.

References

1. Lu, Y. C.; King, F. L.; Duckworth, D. C. Electrochemically-induced reactions of hexafluorophosphate anions with water in negative ion electrospray mass spectrometry of undiluted ionic liquids. J. Am. Soc. Mass Spectrom. 2006,17, (7), 939-944.

2. Harrison, A. G.; Young, A. B. Fragmentation of protonated oligoalanines: Amide bond cleavage and beyond. J. Am. Soc. Mass Spectrom. 2004,15, (12), 1810-1819.

3. Laskin, J.; Denisov, E.; Futrell, J. H. Fragmentation energetics of small peptides from multiple-collision activation and surface-induced dissociation in FT-ICR MS. Int. J. Mass Spectrom. 2002,219, (1), 189-201.

Figure 1S. Fragmentation of singly protonated tetraalanine when the first of the two excitation frequencies is held at 83 kHz, the second excitation frequency is changed between the experiments by an increment of 0.05 kHz. Amplitude of excitation is 2.5 Vpp and relative phase angle is set to 0° for all experimental conditions.

Figure 2S. Fragmentation of singly protonated tetraalanine with a two-frequency excitation waveform at different scan rates when the first of the two excitation frequencies is held at 83 kHz (qz=0.22) and the second excitation frequency is a) 84 kHz and b) 103 kHz. The excitation amplitude is 2.2 Vpp and the relative phase angle of the two frequencies is 0° for all experiments.

Figure 1S

Figure 2S


1