Patent Application
20190371588
This disclosure relates generally to methods and apparatus for tuning mass analyzers. More particularly, this disclosure relates to methods and apparatus for dynamic tuning of Fourier transform (FT) mass analyzers, such as an orbital electrostatic trap mass analyzer or a Fourier Transform Ion Cyclotron Resonance (FTICR) mass analyzer, using plural sets of optimization criteria.
In one version of an orbital electrostatic trap mass analyzer (commercially marketed by Thermo Fisher Scientific under the trademark Orbitrap™) ions are trapped in an orbital motion within a space between an inner, spindle-like electrode and an outer, barrel-like electrode assembly. Different ions oscillate at different frequencies within the orbital electrostatic trap, resulting in their separation over a period of time. The image current from the trapped ions, induced on the outer electrode assembly, is detected and the resulting time-dependent amplitude signal is converted to a frequency spectrum and then to a mass spectrum by processing the data in a manner similar to that used in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The resolving power of an orbital electrostatic trap mass analyzer can be improved by increasing the frequency of ion motion (by, for example, increasing the strength of the electrostatic field) or by increasing the detection period, making it possible to achieve a resolving power up to at least 1,000,000 at nik 200 using currently commercially available orbital electrostatic trap mass analyzers.
Mass analyzer systems, including orbital electrostatic trap and FTICR systems, require proper tuning in order to optimize the voltages that are applied to the various electrodes of the mass analyzer and associated ion optics. The tuning process may be performed one time only, such as for instance at the time the instrument is initially set-up. After the voltages have been optimized, according to a set of criteria, the voltages may be fixed at the optimized values. Typically, the criteria for which the voltages are optimized correspond to high-stress scenarios, e.g., highest permitted resolving power, largest permitted ion population, etc. The rationale for tuning based on high-stress scenarios criteria stems from the fact that the analytical metrics of orbital electrostatic trap and FTICR mass spectra (e.g., resolving power, signal-to-noise ratio, etc.) are determined by the trajectories of the ions that are captured in the analyzer, and how well those trapped ions adhere to certain simplified equations of motion. In particular, the longer the ions are allowed to undergo orbital motion, the better the resolving power. However, it is also generally the case that any deviations in ion motion from the idealized trajectories will be magnified proportional to the amount of time the ions spend in the analyzer. It therefore follows that if ion motion is close-to-ideal for long transients (high resolving power), then it will also be close-to-ideal for shorter transients (lower resolving power).
This traditional approach to tuning an orbital electrostatic trap or FTICR mass analyzer, using optimization criteria that are selected for high-stress scenarios, generally ignores two important realities. First, a majority of users do not operate the instrument at the highest possible resolving power settings. This is especially true in typical proteomics experiments, where the resolving power setting might be only 120,000 (at m/z 200), a factor of at least 2 less than the setting at which the instrument was tuned. Higher resolving powers are not used because the added data does not typically result in analytically useful gains for experiments in which the most important result is the number of peptide identifications. Second, any defects in the analyzer may only be apparent at the longest transient times (highest resolving power settings). Accordingly, the traditional tuning approach optimizes mass analyzer properties that are rarely or never encountered in practice when the instrument is operated using lower resolving power settings.
It would be beneficial to provide methods and apparatus that overcome at least some of the above-mentioned disadvantages and/or limitations.
In accordance with an aspect of at least one embodiment there is provided a method of operating a Fourier Transform (FT) mass analyzer having a plurality of selectable resolving power settings, the method comprising: storing an optimized voltage value in association with each one of the plurality of selectable resolving power settings, wherein the optimized voltage values for at least two of the selectable resolving power settings differ from one another; selecting one of the plurality of selectable resolving power settings; in dependence upon selecting the one of the plurality of selectable resolving power settings, retrieving the optimized voltage value that is stored in association therewith; controlling at least one voltage setting of the FT mass analyzer based on the retrieved optimized voltage value; and performing an analytical scan, at the selected one of the plurality of selectable resolving power settings, for a population of ions within the FT mass analyzer.
In accordance with an aspect of at least one embodiment there is provided a Fourier transform (FT) mass analyzer having an analyzer region within which ions are confined for mass analysis, the FT mass analyzer having a plurality of selectable resolving power settings, and the FT mass analyzer comprising: a voltage source configured to apply a voltage of adjustable amplitude to an electrode of the FT mass analyzer; and a controller, coupled to the voltage source, and being programmed to perform steps of: determining a resolving power setting of the FT mass analyzer at which an analytical scan is to be performed; retrieving from a memory store an optimized voltage value that is stored in association with the determined resolving power setting; and controlling the voltage source, based on the optimized voltage value, to apply a predetermined voltage to the electrode during the analytical scan, wherein the controller controls the voltage source to apply a different predetermined voltage to the electrode for at least two resolving power settings of the plurality of selectable resolving power settings, based on different optimized voltage values stored in association with the at least two resolving power settings and retrieved from the memory store by the controller.
In accordance with an aspect of at least one embodiment there is provided a method of tuning a Fourier Transform (FT) mass analyzer having a plurality of selectable resolving power settings, the method comprising: for each one of the plurality of selectable resolving power settings: varying at least one voltage applied to an electrode of the FT mass analyzer over a range of voltage values; recording a variation of a performance parameter over the applied range of voltage values; identifying an optimized voltage value from the recorded variation of the performance parameter using a selection criterion; and storing the optimized voltage value in association with the corresponding resolving power setting, wherein the optimized voltage values for at least two resolving power settings of the plurality of resolving power settings differ from one another.
The instant invention will now be described by way of example only, and with reference to the attached drawings, wherein similar reference numerals denote similar elements throughout the several views, and in which:
The following description is presented to enable a person skilled in the art to make and use the invention, and is provided in the context of a particular application and its requirements. Various modifications to the disclosed embodiments will be readily apparent to those skilled in the art, and the general principles defined herein may be applied to other embodiments and applications without departing from the scope of the invention. Thus, the present invention is not intended to be limited to the embodiments disclosed, but is to be accorded the widest scope consistent with the principles and features disclosed herein. In particular, it is to be understood that although various embodiments are discussed herein using the specific example of an orbital electrostatic trap mass analyzer, many of the same principles also apply equally well to FTICR-MS and other types of FT mass analyzers.
Throughout the disclosure and in the appended claims, the following terms shall be understood to have the following meanings.
The term “peak coalescence threshold” refers to the signal-to-noise (S/N) ratio just prior to two mass-spectral peaks of interest coalescing completely. For example, and referencing
The term “isotope ratio fidelity” refers to the degree to which an experimentally observed isotope abundance ratio matches the expected isotope abundance ratio.
The term “resolving power” is defined generally as the position of a peak divided by the full width of the peak at half the maximum height (FWHM). In a mass spectrum, “resolving power” then means the mass-to-charge ratio that is assigned to a peak in a mass spectrum, divided by the full width of the peak at half the maximum height (FWHM). Resolving power is expressed as a dimensionless value.
The term “resolving power setting,” which may be used interchangeably with the term “orbital electrostatic trap resolution” or “FT resolution” or simply “resolution,” refers to a user-selectable operating parameter for an orbital electrostatic trap or for another type of FT-MS system. Selecting a particular resolving power setting for experimental data acquisition (i.e., an analytical scan) causes the system to detect the ion image current for a period of time that is sufficient to achieve a desired resolving power for a specific mass-to-charge value, such as for instance m/z 200. For example, typical resolving power settings for current orbital electrostatic trap systems may be 120,000, 240,000, 500,000 and 1,000,000, etc., at m/z 200. For current commercially available mass spectrometers, the operator may select one of several discrete values of resolving power settings for a particular scan, but in alternative implementations the resolving power setting may be selectable as a value lying within a continuous range of achievable resolving power.
Referring now to
Those skilled in the art will recognize that although voltage source 16 is indicated in
Traditionally, an orbital electrostatic trap mass analyzer system such as the one that is shown in
A tailored approach to orbital electrostatic trap tuning offers the potential to improve important performance metrics when the orbital electrostatic trap is being operated using certain settings. For example, a unique set of tuning parameters may be determined for operation at low resolving power, so as to maximize the peak coalescence threshold when operating at low resolving power while keeping other metrics such as isotope ratio fidelity and signal-to-noise ratio within acceptable ranges. A separate tuning operation may be performed for every different selectable resolving power setting. However, in practice it is also possible that the same set of tuning parameters may apply to a range of different selectable resolving power settings. For instance, a first set of tuning parameters may be appropriate for resolving power settings of 120,000 and 240,000 at m/z 200, and a second set of tuning parameters may be appropriate for resolving power settings of 500,000 and 1,000,000 at m/z 200.
A multi-level tuning approach, suitable for tuning the orbital electrostatic trap mass analyzer shown in
A multi-level tuning approach allows a user to shape and control the motion of ions within the mass analyzer, in order to encourage or discourage certain behavior in a way that is variably visible depending upon transient length. For example, the orbital electrostatic trap deflector voltage may be changed so as to allow ions to obtain motion that promotes better behavior with respect to peak coalescence. Although this behavior may lead to decreased performance with respect to other metrics, these other metrics may only be apparent or useful at longer transients. Thus, when the orbital electrostatic trap is operated using a lower resolving power setting, and therefore a relatively shorter transient is acquired, the affected portion of the data is effectively eliminated.
Referring now to
The method discussed above with reference to
Referring now to
Due to the small differences that exist between different FT mass analyzer instruments (for example, small differences between two different orbital electrostatic trap mass analyzer instruments), which result from manufacturing tolerances, environmental conditions, etc., it will normally be necessary to perform the method that is discussed with reference to
In an alternative embodiment, a “tuning curve” may be constructed using data that are acquired at a plurality of different resolving power settings. For example, an optimized deflector voltage value may be determined for achieving improved isotope fidelity performance at each of the plurality of resolving power settings, and then an optimized value may be selected for a resolving power that is intermediate two of the tuning data points by extrapolation using the tuning curve. By way of a specific and non-limiting example, a tuning curve may be constructed from data that are acquired at resolving powers of 50,000, 100,000, 250,000 and 1,000,000, and optionally saved at step 300 of the method shown in
Advantageously, changing the mass analyzer properties “on-the-fly” in the manner that is described supra does not introduce meaningful penalties in terms of analysis speed, since acquisition times (typically on the order of a few tens to several hundreds of milliseconds) are far longer than settling times (typically a few tens of microseconds) for the power supplies that are used to provide the voltages to the various electrodes in an orbital electrostatic trap system. Of course, changing the analyzer properties “on-the-fly” will necessitate the contemporaneous adjustment of other important aspects of experimental operation, such as for instance mass calibration parameters. Fortunately, such properties may be calibrated prior to running experiments and therefore this requirement also poses no significant difficulties for experimental operation.
The following examples are provided to illustrate specific and non-limiting applications in which the above-mentioned tuning process may be used to improve performance metrics of FT mass analyzers, such as for instance an orbital electrostatic trap mass analyzer.
Peak coupling is known to affect the quality of the mass spectra that are obtained using an orbital electrostatic trap mass analyzer. This effect causes spectral peaks arising from ions of similar frequency to move toward each other as the number of ions associated with those peaks increases. For instance, peak coupling is observed in the isotope envelope of +1 charge states, causing even the A+3 or A+4 peaks to be shifted toward the monoisotopic peak by as much as 10-20 ppm.
The strength of the peak coupling effect can be changed by changing the voltages that are applied to the various electrodes in the orbital electrostatic trap mass analyzer. These voltages are typically set according to a tuning procedure that is principally concerned with optimizing the performance of the orbital electrostatic trap in terms of the isotope ratio fidelity. Isotope ratio fidelity usually decreases with longer transient periods, and therefore the tuning procedure is usually conducted at the longest available transient setting (highest available resolving power). Unfortunately, the voltage settings that result in optimum isotope ratio fidelity behavior also usually increase the peak coupling strength, which leads to a decrease in the coalescence threshold. However, at lower resolving power settings isotopic ratio fidelity may be good enough to allow for some flexibility in optimizing analyzer behavior according to other metrics, for example coalescence threshold.
As will be apparent, when the orbital electrostatic trap analyzers are operated at a resolving power setting of 500,000 or 1,000,000, then no improvement is expected relative to operation using the traditional tuning approach in which optimization criteria are selected for worst case scenarios. However, when the orbital electrostatic trap analyzers are operated at a resolving power setting of 120,000 or 240,000, then in this example an improvement in the peak coalescence threshold by up to a factor of two may be realized whilst still providing acceptable isotope ratio fidelity. This improvement provides a significant advantage for users who do not use the highest resolution settings on their instruments. In particular, the problem of charge states being rendered unassignable due to strong peak coupling, which causes large movements of the peaks in the mass spectrum, can be largely avoided. This is advantageous of course, since the inability to correctly assign charge states can complicate or even render inoperative downstream bioinformatics approaches that rely on correct functioning of charge state and monoisotopic mass assignment.
Referring now to
The preceding disclosure describes an operational scheme in which various orbital electrostatic trap ion injection and/or ion capture parameters—such as for instance the deflector electrode voltage, the injection offset (C-trap offset), lens 6 voltage, etc.—are given different values optimized to different resolving power settings. Other parameters such as ion population and mass range could also be used, and other components could be included in the list of components with different values optimized for each resolving power setting. Throughout this disclosure the selection of optimized values for different resolving power settings has been described in term of increasing orbital electrostatic trap performance with respect to peak coupling and coalescence. However, the same principles could be applied in order to improve orbital electrostatic trap performance with respect to some other key metric. Finally, while this disclosure focuses on orbital electrostatic trap instruments specifically, most FTMS instruments are operated in a similar way, with all settings remaining the same no matter the resolution, and therefore the same principles could be applied to other FTMS analyzers as well (such as FTICR-MS analyzers).
As used herein, including in the claims, unless the context indicates otherwise, singular forms of the terms herein are to be construed as including the plural form and vice versa. For instance, unless the context indicates otherwise, a singular reference, such as “a” or “an” means “one or more”.
Throughout the description and claims of this specification, the words “comprise”, “including”, “having” and “contain” and variations of the words, for example “comprising” and “comprises” etc., mean “including but not limited to”, and are not intended to (and do not) exclude other components.
It will be appreciated that variations to the foregoing embodiments of the invention can be made while still falling within the scope of the invention. Each feature disclosed in this specification, unless stated otherwise, may be replaced by alternative features serving the same, equivalent or similar purpose. Thus, unless stated otherwise, each feature disclosed is one example only of a generic series of equivalent or similar features.
The use of any and all examples, or exemplary language (“for instance”, “such as”, “for example”, “e.g.” and like language) provided herein, is intended merely to better illustrate the invention and does not indicate a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
Any steps described in this specification may be performed in any order or simultaneously unless stated or the context requires otherwise.
All of the features disclosed in this specification may be combined in any combination, except combinations where at least some of such features and/or steps are mutually exclusive. In particular, the preferred features of the invention are applicable to all aspects of the invention and may be used in any combination. Likewise, features described in non-essential combinations may be used separately (not in combination).
