Use of notched broadband waveforms in a linear ion trap

Details Use of notched broadband waveforms in a linear ion trap Use of notched broadband waveforms in a linear ion trap

2002-12-19

2004-11-09

Lee, John R. (Department: 2881)

Radiant energy

Ionic separation or analysis

Cyclically varying ion selecting field means

C250S287000, C250S282000, C250S281000, C250S290000, C250S293000, C250S299000

Reexamination Certificate

active

06815673

ABSTRACT:

FIELD OF THE INVENTION
This invention relates to mass spectrometry, and more particularly is concerned with a method of analyzing ions using mass spectrometers where at least one of the quadrapoles is operated as a linear ion trap.
BACKGROUND OF THE INVENTION
The development of linear radio frequency (RF) multipole technology has led to significant improvements in sensitivity for those mass spectrometers which are coupled to continuous ionization sources (e.g. electrospray) but operate in a pulsed fashion, such as orthogonal time-of-flight (oTOF) devices, Paul ion traps, and Fourier Transform Ion Cyclotron Resonance (FTICR) traps. Multipoles located upstream of the mass analyzer may be operated as storage devices such that ions produced from the source are trapped while ions in the mass spectrometer are scanned. In this manner, instrument duty cycle, and therefore sensitivity, is improved. Sensitivity gains using multipole ion storage capabilities coupled to oTOF devices are detailed in U.S. Pat. No. 5,689,111 (Dresch et al.), U.S. Pat. Nos. 6,020,586 and 6,011,259 (Whitehouse et al.) as well as PCT WO 00/33350 (Douglas et al.) Multipoles coupled to Paul ion traps are documented by Douglas (U.S. Pat. No. 5,179,278), Cha et al. (Anal. Chem. 2000, 72, 5647-5654), and Whitehouse et al. (U.S. Pat. No. 6,121,607) while multipoles coupled to FTICR traps are reported by Senko et al. (J. Am. Soc. Mass Spectrom. 1997, 8, 970-976), and Belov et al U. Am. Soc. Mass Spectrom. 2001, 12, 38-48; Anal. Chem. 2001, 73, 253-261).
A further benefit of operating multipoles as ion storage devices is that ion trajectories may be manipulated through the application of auxiliary RF fields. Most techniques involving such ion-trajectory manipulation use an electrode configuration, which generates a quadrupole electric field because the characteristics of ion motion can be predicted most accurately in this environment. The characteristic motion of ions with stable trajectories in an RF quadrupole field allow them to be excited resonantly, in a mass-selective way, through the application of auxiliary RF fields. The consequences of resonant excitation, whether collision activated dissociation (CAD) or collisions with electrodes, can be controlled, to some degree, by adjusting the amplitude of the auxiliary RF signal. Consequently, those skilled in the art often use auxiliary RF fields for applications involving (i) precursor ion isolation via the resonance ejection of all unwanted ions, (ii) resonant excitation of the isolated precursor ion to promote the formation of specific fragment ions from the said precursor ion by collision activated dissociation. Finally, in those cases where such isolation and excitation occur in a device, which is capable of mass-selective detection, an auxiliary RF signal is applied to facilitate mass-selective ion ejection for the purposes of detection.
Two well-known mass spectrometer designs include the triple-stage quadrupole mass spectrometer and the quadrupole orthogonal time of flight mass spectrometer (Qq-oTOF), both of which consist of a plurality of quadrupoles, any one of which may be utilized as a linear ion trap (LIT). One of the earliest reports for using a quadrupole as a linear ion trap in a triple-stage quadrupole arrangement originated from G. G. Dolnikowski, M. J. Kristo, C. G. Enke, and J. T. Watson (Int. J. of Mass Spectom. and Ion Processes 82 (1988) 1-15) wherein product ions in the collision cell were stored by raising the potential of an inter-quadrupole aperture lens above the DC offset voltage of the quadrupole. J. Throck Watson, D. Jaouen, H. Mestdagh, and C. Rolando (Int. J. of Mass Spectrom. and Ion Processes 93 (1989) 225-235) described using a Nermag multi quadrupole mass spectrometer to study ion/molecule reactions, wherein ions were ejected in a mass-selective way from the collision cell by supplying auxiliary RF power at selected frequencies.
In contrast, Douglas in U.S. Pat. No. 5,179,278 teaches that a plurality of frequency components comprising a noise spectrum may be applied to a LIT to eject radially a broad range of masses such that ions may be accumulated in a mass-selective way by a Paul trap located down-stream. In PCT patent WO 00/33350, Douglas et al describe utilizing the collision cell in a triple-stage quadrupole as a LIT wherein axial acceleration of a mass resolved precursor ion into the trap causes fragmentation (MS/MS). Once fragment ions and unfragmented precursors are stored in the trap, a notched broadband waveform is applied to isolate an ion of interest for another stage of MS induced via radial excitation CAD. The LIT isolation/dissociation can occur over several cycles for MS capabilities. Ions are then passed to Q
3
for mass analysis. PCT WO 00/33350 further discloses the ability to perform identical operations in a Qq-oTOF, with initial precursor ion selection performed in Q
1
and mass analysis provided by the TOF.
Other examples of coupling LITs to oTOF mass analyzers are provided in U.S. Pat. No. 6,011,259 (Whitehouse et al) and U.S. Pat. No. 6,020,586 (Dresch et al). However, unlike the patent of Douglas et al (PCT WO 00/33350), there is no Q
1
precursor ion selection. Notably, Q
1
precursor ion selection with axial acceleration into a collision cell is preferred over radial excitation of a previously trapped precursor to create the first generation spectrum because more kinetic energy is available to fragment the precursor through axial acceleration. The ability to adjust the collision energy over a broad range allows the relative abundance of fragment ions to be controlled.
In the LIT configurations above, notched broadband waveforms or auxiliary RF are applied for the purpose of resonant ejection after ions are trapped, and not during the accumulation period. It is well known that ions in the fringing region have poorly defined trajectories and are easily lost. It is possible that this technique has not been used previously because it was thought that an auxiliary waveform, applied during the fill, would result in increased losses in the fringing region, but this is demonstrably not so. Accordingly, prior art linear ion trap configurations have been designed to apply notched broadband waveforms or auxiliary RF after ions have been accumulated by the ion trap.
There are several disadvantages associated with delaying until the fill is complete. Specifically, as charge accumulates, heavier ions can be lost preferentially. By accumulating the ion of interest, which may be a heavier ion, this undesirable loss of intensity is avoided. Similarly, a low intensity fragment cannot be accumulated preferentially unless the broadband is applied during the fill. In consequence, the space-charge limit could be reached before a sufficient number of the fragments of interest had accumulated. Also, duty cycle is degraded by waiting until after the fill to isolate the ion(s) of interest. Finally, in some cases, undesirable chemistry may occur among different fragments. By ejecting unwanted fragments as soon as they are formed, the probability of undesirable chemistry is reduced considerably.
SUMMARY OF THE INVENTION
The present invention provides a method of analyzing a substance in a mass spectrometer apparatus comprising an ion source, a quadrupole ion guide, and a linear ion trap, the method comprising the steps of:
(a) ionizing the substance to generate a stream of ions;
(b) supplying the stream of ions to the quadrupole ion guide to select ions within a broad range of mass-to-charge ratios;
(c) providing the stream of ions from the quadrupole ion guide to the linear ion trap for the generation and accumulation of fragment ions;
(d) simultaneously with step (c) applying a notched broadband waveform having a first notch width to the linear ion trap to select fragment ions within a predetermined mass range; and
(e) analyzing the fragment ion spectrum after accumulation.
The present invention also provides an apparatus for analyzing a substance, the apparatus comprising:
(a) an ion source for generating a stream of ions;
(

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