Implementation of Precursor and Neutral Loss Scans on a Miniature Ion Trap Mass Spectrometer and Performance Comparison to a Benchtop Linear Ion Trap
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Implementation of orthogonal double resonance precursor and neutral loss scans on the Mini 12 miniature rectilinear ion trap mass spectrometer is described, and performance is compared to that of a commercial Thermo linear trap quadropole (LTQ) linear ion trap. The ac frequency scan version of the technique at constant rf voltage is used here because it is operationally much simpler to implement. Remarkably, the Mini 12 shows up to two orders of magnitude higher sensitivity compared to that of the LTQ. Resolution on the LTQ is better than unit at scan speeds of ~ 400 Th/s, whereas peak widths on the Mini 12, on average, range from 0.5 to 2.0 Th full width at half maximum and depend heavily on the precursor ion Mathieu q parameter as well as the pump down time that precedes the mass scan. Both sensitivity and resolution are maximized under higher pressure conditions (short pump down time) on the Mini 12. The effective mass range of the product ion ejection waveform was found to be 5.8 Th on the Mini 12 in the precursor ion scan mode vs. that of 3.9 Th on the LTQ. In the neutral loss scan mode, the product ion selectivity was between 8 and 11 Th on the Mini 12 and between 7 and 8 Th on the LTQ. The effects of nonlinear resonance lines on the Mini 12 were also explored.
KeywordsMiniature mass spectrometer MS/MS Tandem mass spectrometry Precursor ion scan Neutral loss scan
Although product ion scans are common on single quadrupole ion traps, the two other main MS/MS scans (precursor scan and neutral loss scan)  are generally thought problematic on a single analyzer. Conventionally, these two survey scans are implemented on triple quadrupole mass spectrometers  wherein the first and third quadrupoles mass select particular precursor and product ions while an intermediate rf-only quadrupole serves as a collision cell. Such a scan is complicated on most single mass analyzers due to the difficulty in not only mass selecting multiple ions simultaneously, but also activating the precursor ion via collision-induced dissociation. A single quadrupole ion trap, however, can do both and hence can perform precursor and neutral loss scans via double resonance, that is, by simultaneously activating precursor ions and ejecting mass-selected product ions by applying multiple resonance (i.e., low-voltage auxiliary) frequencies [3, 4, 5, 6].
Although single analyzer precursor and neutral loss scans do not compare favorably with data-dependent methods  on commercial mass spectrometer systems in terms of mass spectral resolution, sensitivity, and speed, they are more attractive on some miniature systems (see Introduction S1 in SI). Not only does the mass analyzer need to decrease in size on these smaller spectrometers [8, 9, 10, 11, 12], but so do the electronics and data acquisition systems, the ion optics (if there are any), and most importantly, the vacuum system. Because small vacuum pumps, usually a 10 L/s turbo pump backed by a 5 L/min diaphragm pump , struggle to pump a single chamber to < 1 Torr with a continuous atmospheric pressure interface, the discontinuous atmospheric pressure interface (DAPI) has become an attractive alternative [14, 15]. Continuous interfaces do exist on miniature spectrometers, but they are usually 2–3 orders of magnitude less sensitive than their discontinuous counterparts (e.g., Mini 10, 11, 12, S) [16, 17, 18, 19, 20]. Although efforts have been made to miniaturize ICRs , the Orbitrap , sector instruments [23, 24], and even a triple quadrupole mass spectrometer , for the reasons above—especially vacuum system constraints—the quadrupole ion trap has become the predominant analyzer for miniaturization. Conventionally, this would limit miniature mass spectrometers to the full scan mode and the product ion scan mode, and in combination with the long pump down time characteristic of DAPI systems (10−1–100 s), reconstructing precursor and neutral loss spectra from data-dependent sets of product ion scans becomes less feasible. However, if operated unconventionally in the ac frequency scan mode [26, 27, 28], precursor and neutral loss scan modes become available, somewhat mitigating the need for another analyzer for higher resolution or improved MS/MS capabilities and providing an attractive alternative over conventional data-dependent modes.
In this study, we implemented capabilities for precursor ion scanning and neutral loss scanning on a Mini 12 miniature rectilinear ion trap mass spectrometer and compared their performance to that obtained on a commercial Thermo linear trap quadropole (LTQ) linear ion trap. Both resolution and limit of detection were characterized as well as detection efficiency and mass-to-charge selectivity. Nonlinear resonance lines were also explored.
Amphetamine (m/z 136), methamphetamine (m/z 150), 3,4-methylenedioxyamphetamine (m/z 180), 3,4-methylenedioxymethamphetamine (m/z 194), and 3,4-methylenedioxyethylamphetamine (m/z 208) were purchased from Cerilliant (Round Rock, TX, USA). HPLC grade methanol was purchased from Fisher Scientific (Hampton, NH, USA). Formic acid was purchased from Sigma-Aldrich (St. Louis, MO, USA). All analytes were diluted in methanol with 0.1% formic acid. A concentration of 1 ppm was used for all experiments except when a calibration curve was made.
Nanoelectrospray ionization using a 1.5-kV potential was utilized for all experiments. Borosilicate glass capillaries (1.5-mm O.D., 0.86-mm I.D.) from Sutter Instrument Co. (Novato, CA, USA) were pulled to 2-μm tip diameters using a Flaming/Brown micropipette puller (model P-97, Sutter Instrument Co.). The nanospray electrode holder (glass size 1.5 mm) was purchased from Warner Instruments (Hamden, CT, USA) and was fitted with 0.127-mm-diameter silver wire, part number 00303 (Alfa Aesar, Ward Hill, MA), as the electrode.
The Mini 12 uses a discontinuous atmospheric pressure interface . Ions and neutrals are admitted into the Mini 12 RIT by opening the DAPI valve for ~ 12 ms, after which the valve is closed and a wait time is used for collisional cooling. During this time, the pressure in the ion trap drops from 10−1 Torr to between 10−3 and 10−5 Torr, during which mass analysis or collision-induced dissociation takes place.
The performance of the Mini 12 was compared to that of a commercial LTQ linear ion trap mass spectrometer (Thermo Finnigan, San Jose, CA, USA). The LTQ has a three-section linear ion trap with hyperbolic cross sections. The dimensions of the device are x0 = 4.75 mm, y0 = 4 mm, and three axial sections of lengths 12, 37, and 12 mm. The rf was tuned to 1.166 MHz. The LTQ uses helium (ion gauge reading 0.60 × 10−5 Torr) as the cooling and collision gas, whereas the Mini 12 uses air with a base pressure of 10−5 Torr. Importantly, the Mini 12 uses a single-electron multiplier with conversion dynode as the detector, whereas the LTQ uses two, one on either side of the linear ion trap.
The Mini 12 rf circuit was modified as shown in Fig. 1, in red. A center-tapped iron core toroidal transformer (Laird Technologies LFB090050-000, Earth City, MO, USA) enabled coupling of low-voltage ac signals on the y electrodes. The coils on the toroid do not overlap in order to improve isolation between the rf and ac signals. The ac signal is applied to the primary winding, and the two outputs of the secondary winding are applied to the two y rods, giving a dipolar ac signal between the rods. The rf signal is a single phase on the y rods, and low-voltage ac signals are applied directly to the x rods. The LTQ rf coil was modified as described previously [5, 6] with an extra Thermo LTQ low pass filter board (part 97055−91120) and Thermo LTQ balun board (part 97055−91130) in order for low-voltage ac signals to be applied to both x and y electrodes of the linear ion trap.
Two Keysight 33612A arbitrary waveform generators (Newark element14, Chicago, IL, USA) were used to apply low-voltage ac waveforms to the x and y electrodes of each linear ion trap. One generator supplied the waveform for the x electrodes and one supplied the waveform for the y electrodes. The sampling rate of arbitrary waveforms was set at 10 megasamples per second.
Precursor ion scans require application of (1) an ac frequency sweep (at constant rf voltage) for mass-selective precursor ion excitation and (2) a fixed frequency of higher amplitude for ejection of a particular product ion [3, 5, 34]. Neutral loss scans require three simultaneous and identical frequency sweeps with appropriate trigger delays: a first sweep for precursor ion excitation, a second sweep for ejection of leftover precursor ions into the y electrodes, and a third frequency sweep for ejection of the neutral loss product ions in the x dimension. The trigger delay between precursor excitation and product ion ejection is directly proportional to the neutral loss. Generally, excitation amplitude was 200–300 mVpp and ejection amplitude was 600–800 mVpp. Excitation and artifact rejection signals were applied to the y rods and ejection signals were applied to the x rods, usually each in a dipolar fashion. All frequency sweeps in this work are inverse Mathieu q scans  that linearize the mass scale with respect to time by sweeping the ac frequency nonlinearly. These waveforms generally started at Mathieu q = 0.908 and ended at q = 0.3 with a sweep time of 600 ms. They were calculated in Matlab according to previously described methods  and imported to the Keysight waveform generators.
The Mini 12 scan function is as follows: ion injection (DAPI open), 12 ms; cooling (DAPI closed, instrument pump down), 700 ms; ramp rf voltage up to operating point, 100 ms; mass scan, 600 ms; reset for next scan, 1 ms. The function generators were triggered by a 5-V pulse that normally operates the “Sample Pump” as a 24-V pulse. A voltage divider was used to obtain the former from the latter. Data were acquired at 312,500 samples per second and were digitally smoothed using a 30-point triangle filter.
The LTQ was operated in the “Ultrazoom” mode with an ion injection time of 10 ms. The rf voltage was constant throughout the ion injection, cooling, and mass scan and was controlled externally by substituting the coil modulation signal (proportional to the rf amplitude) on the rf detector board with a dc signal from an external function generator. Automatic gain control was turned off throughout this study, but space charge was not observed at 1-ppm concentration as demonstrated in SI Figure S1. The three function generators were triggered by the “Injection” trigger in the LTQ Tune “Diagnostics” menu. The data collection rate on the LTQ was approximately 2700 samples per second.
In all experiments, m/z 119 had its working point at a Mathieu q value of 0.57 on LTQ vs. 0.53 on the Mini 12.
Data were analyzed in either Matlab (Mathworks, Natick, MA, USA) or Excel (Microsoft, Redmond, WA, USA). Spectra were mass calibrated separately using a linear fit of m/z vs. time. In most cases, Mini 12 spectra are the average of three separate scans, whereas the LTQ data is the average of 10 scans. In the case of the LTQ, the only scan saved was the average spectrum and hence error bars will not be shown for LTQ data. All ion intensities are baseline-subtracted integrated intensities. Resolution is dimensionless and is reported as m/Δm, where m is the m/z value of the precursor ion (Th) and Δm is the measured full (peak) width at half maximum intensity (FWHM), also in Th.
Results and Discussion
Performance of Precursor and Neutral Loss Scans on LTQ (helium bath gas) and Mini 12 (air)
Mini 12 Pre
Mini 12 NL
Resolution (m/Δm) at m/z 150
Product ion selection window (m/z 136, m/z 150)
3.9, 4.3 Th
5.6, 5.6 Th
7.1, 7.8 Th
8.6, 11 Th
Limit of detection (ppb)a
Performance of Precursor and Neutral Loss Scans
Both precursor ion scans of m/z 119 (for amphetamine and methamphetamine) and m/z 163 (for the other three) are shown in Fig. 2b, c. A double simultaneous precursor ion scan is then shown in Fig. 2d. This spectrum was obtained by applying the resonance frequency of m/z 119 on one of the x rods and simultaneously applying the resonance frequency of m/z 163 on the other x rod while sweeping the excitation frequency on the y rods. The corresponding neutral loss scans of 17 and 31 Da are shown in panels e and f. Note that m/z 163 (a fragment of m/z 180, 194, and 208) is detected because it fragments to m/z 133 and 135 and the neutral loss scan does not have unit selectivity. Corresponding precursor and neutral loss scans on the LTQ are shown in Figure S2 (helium bath gas) and Figure S3 (nitrogen bath gas). The use of nitrogen as bath gas increases the integrated signal intensity but also compromises resolution.
Sensitivity and Limit of Detection
The remarkable difference between limits of detection on the Mini 12 and LTQ in the precursor ion scan mode can likely be explained by several factors. First, the Mini 12 uses air as collision gas whereas the LTQ uses helium, which affects fragmentation efficiency and collisional damping (the latter being important to cool the product ions to the center of the trap before they are ejected in the x dimension). The higher operating pressure on the Mini 12 helps with these processes. Substituting nitrogen for helium in the LTQ gave a limit of detection of 250 ppb on the LTQ in the precursor ion scan mode (Figure S5a), and the sensitivity (slope of the calibration curve) increased by a factor of 2.6 for m/z 136 and 5.8 for m/z 150.
A calibration curve was also constructed for the neutral loss scan of 31 Da. Solutions used for this experiment consisted solely of methamphetamine and 3,4-methylenedioxymethamphetamine at various concentrations. The calibration curve on the Mini 12 for both m/z 150 and 194 is shown in Fig. 3b. Surprisingly, even at 1 ppm concentration, there is loss of calibration linearity. The limit of detection (S/N = 3) was found to be 250 ppb, much higher than that of the precursor ion scan and reasonably comparable to the LTQ’s 500-ppb detection limit in the neutral loss scan mode using helium as bath gas (Fig. 3d). Using nitrogen as bath gas on the LTQ resulted in a limit of detection of 250 ppb (Figure S5b) due to a doubling in sensitivity.
Both the severe increase in limit of detection and loss of calibration curve linearity on the Mini 12, even at high concentrations (1 ppm), are somewhat puzzling. Space charge may play a role here but is unlikely to be the only factor since it was not observed at 1 ppm in the full scan mode or in the other MS/MS scan modes on the Mini 12 and LTQ. However, there are key differences between the precursor scan and neutral loss scan that are worth considering. We postulate that the loss in calibration linearity is due to frequency shifts in the Mini 12 ion trap [36, 37]. As the precursor ions are excited, they approach the y electrodes where their secular frequencies shift. Because the product ions are then generated close to the y electrodes, their secular frequencies are shifted relative to their “true” or predicted secular frequencies. Their y oscillations then dampen rapidly in the ion trap due to collisions with air molecules, returning their secular frequencies to the “normal” predicted values. At the same time, their x amplitudes increase via the ejection frequency sweep, again shifting their frequencies. It is this combination of frequency shifts, exacerbated by the fact that the precursor and product ion ejection waveforms must be swept at a constant mass offset that may cause loss of calibration linearity and also an increase in limit of detection.
Resolution and Product Ion Selectivity
Resolution in ac frequency scanning depends heavily upon the frequency dispersion of the trapped ions as well as their secular frequency bandwidths . It is thus important to characterize both mass spectral resolution and the product ion selection window.
At an rf amplitude of 7000 DAC units (LMCO ~ 70 Th), peak widths on the Mini 12 were 1.48 and 1.86 Th for m/z 136 and 150, respectively, whereas for an rf amplitude of 9500 DAC units (LMCO ~ 92 Th), peak widths decreased to 0.93 and 0.87 Th. Unfortunately, at higher rf amplitudes, artifact peaks were observed because the amphetamine precursor ions fragment to m/z 91 as well, and so if the precursors fragment while the LMCO > 91 Th, the product ion m/z 91 will inadvertently be detected by boundary instability. In the case of the LTQ, unit resolution was observed for a LMCO of 87 Th, with approximate peak widths of 0.5 Th for m/z 136 and 150. In nitrogen, the peak width for m/z 136 was 1.1 Th and for m/z 150 was 0.9 Th. On both the Mini 12 and LTQ, resolution degraded at lower Mathieu q values due to decreased secular frequency dispersion.
In order to determine the product ion selection window (in Th) for the neutral loss scan of 31 Da, the trigger delay between the precursor excitation frequency sweep and both the artifact rejection sweep and product ejection sweep was varied while keeping the difference between the artifact rejection trigger delay and product ejection trigger delay constant. The same rf amplitude, frequency scan rate, and ac voltages were used in this experiment as compared to those of the precursor scan experiment. The integrated intensities of methamphetamine and 3,4-methylenedioxymethamphetamine were plotted with respect to the trigger delays, and the results are shown in Fig. 5c (Mini 12) and d (LTQ, helium). For the Mini 12, the approximate product ion selection windows were 8.6 and 11 Th for m/z 150 and 194, respectively. For the LTQ, those widths were 7.1 and 7.8 Th, respectively. Other factors, such as mass scanning rate, that affect resolution are mentioned in Discussion S2.
Effect of Cooling Time
Although not a significant concern on a benchtop instrument which operates at constant pressure in the ion trap volume, pump down time on the Mini 12 must be carefully considered. The Mini 12 uses a discontinuous atmospheric pressure interface  composed of a silicone tube that is constricted by a pinch valve except for when ions are introduced. During ion introduction, a low-voltage pulse opens the valve, thereby letting ions and neutrals into the vacuum chamber. The ions are then trapped and cooled, and the chamber is pumped down to operating pressure. Because the pressure in the Mini 12 varies as a function of time, it is critical to optimize it for the given scan mode.
Nonlinear Resonance Lines
Precursor and neutral loss scans using orthogonal double resonance excitation have been successfully implemented on a miniature rectilinear ion trap. Compared to a selected benchtop instrument, the Mini 12 offers up to two orders of magnitude higher sensitivity in the precursor scan mode and 2× better sensitivity in the neutral loss scan mode. Future work should focus on improving the product ion selection window, which limits the selectivity of both types of MS/MS scans, as well as reducing the contribution of artifact peaks (from boundary instability).
The scans demonstrated here are particularly valuable for miniature instruments that use discontinuous interfaces, as they have very low duty cycles and will also be expected to have higher sensitivity by using a heavier collision gas. A goal of this work is to implement these scan modes at NASA Goddard Space Flight Center for possible use in future planetary missions [45, 46]. This would build on the importance of mass spectrometry in many NASA and European Space Agency missions including the Rosetta project [47, 48] and the more recent development of the Sample Analysis at Mars suite and Mars Organic Molecule Analyzer [49, 50].
Rob Schrader (Purdue University) is thanked for the Table of Contents graphic.
The authors acknowledge funding from NASA Planetary Sciences Division, Science Mission Directorate (NNX16AJ25G). This work was also supported by a NASA Space Technology Research Fellowship (DTS).
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