METHODS FOR OPERATING ELECTROSTATIC TRAP MASS ANALYZERS

Abstract

A system comprises an electrostatic trapping mass analyzer and an information processor configured to receive a transient signal from the electrostatic trapping mass analyzer at a maximum resolution, the information processor comprising instructions operable to: partition the transient signal into segments and, while a quality metric is either less than a pre-determined minimum threshold or greater than a pre-determined maximum threshold value, to perform the steps of: (i) defining a test transient as being equal to either a first one of the segments or a previously defined transient with an appended signal segment; (ii) generating a spectrum of component frequencies by calculating a mathematical transform of the test transient; and (iii) determining the quality metric from the spectrum of component frequencies; and set an instrumental resolution to be employed for subsequent mass spectral data acquisitions in accordance with a length of the most-recently-defined test transient.

Claims

1. A mass spectrometer system comprising: an ion source; an electrostatic trapping mass analyzer configured to trap ions received from the ion; a computer or information processor configured to receive a transient signal that is output from the electrostatic trapping mass analyzer with said electrostatic trapping mass analyzer operated at its maximum resolution, the computer or information processor comprising computer readable instructions operable to: partition the transient signal into signal segments; define a test transient as being equal to a first one of the segments; calculate a mathematical transform of the test transient and thereby generate a spectrum of component frequencies of the test transient; determine a quality metric from the spectrum of component frequencies and compare the quality metric to either a pre-determined minimum threshold value or a pre-determined maximum threshold value; perform, while the most-recently-determined quality metric is either less than the pre-determined minimum threshold value or greater than the pre-determined maximum threshold value, the steps of: appending a next signal segment onto the test transient; re-defining the test transient as being the previously-defined test transient having the appended next signal segment appended thereto; calculating a mathematical transform of the test transient and thereby generating a new spectrum of component frequencies of the test transient; and re-determining the quality metric from the new spectrum of component frequencies; and set an instrumental resolution to be employed for subsequent mass spectral data acquisitions by the electrostatic trapping mass analyzer in accordance with a length of the most-recently-defined test transient.

2. A system as recited in claim 1, wherein the electrostatic trapping mass analyzer comprises a Cassinian trap mass analyzer.

3. A system as recited in claim 1, wherein the electrostatic trapping mass analyzer comprises a trapping region defined by: an inner spindle electrode having an outer surface that is axially symmetric about the longitudinal axis and that is symmetric about a central equatorial plane that is perpendicular to the longitudinal axis; and a pair of outer electrodes disposed at either side of the equatorial plane and having respective inner surfaces, wherein the outer surface of the inner spindle electrode and the inner surfaces of the outer electrodes are shaped such that a trapping potential corresponding to the trapping field is a quadro-logarithmic potential that is established by application of an electrostatic voltage difference between the inner spindle electrode and the outer electrodes.

4. A system as recited in claim 1, wherein the computer readable instructions are further operable to generate a respective mass spectrum from each spectrum of component frequencies by calibrating each spectrum of component frequencies in units of mass-to-charge ratio (m/z).

5. A system as recited in claim 1, wherein each determination of the quality metric by the computer readable instructions is based on one or more of an overall spectral signal-to-noise ratio, a ratio of intensities of two particular spectral peaks and a full-width-at half maximum evaluation of one or more peak widths.

6. A mass spectrometer system comprising: an ion source; an electrostatic trapping mass analyzer configured to trap ions received from the ion; a computer or information processor configured to receive a transient signal that is output from the electrostatic trapping mass analyzer and that is defined over a time domain extending from a first end at time .sub.0 to a second end at time .sub.m, where .sub.0<.sub.m, the computer or information processor comprising computer readable instructions operable to: define a test transient as being equal to the retrieved transient signal; truncate the previously-defined test transient by eliminating a segment of the previously-defined test transient from the second end of the previously-defined test transient; generate a test spectrum from the test transient by calculating a mathematical transform of the test transient ; determine a quality metric from the test spectrum; perform, while the most-recently-determined quality metric is either less than a pre-determined minimum threshold value or greater than a pre-determined maximum threshold value, the steps of: truncating the previously-defined test transient by eliminating a segment of the previously-defined test transient from the end of the previously-defined test transient that is opposite to the first end; generating a test spectrum from the test transient by calculating a mathematical transform of the test transient; and determining the quality metric from the test spectrum; set a transient length equal to a length of the test transient prior to most recent truncation; and set an instrumental resolution to be employed for subsequent mass spectral data acquisitions in accordance with the transient length.

7. A system as recited in claim 6, wherein the electrostatic trapping mass analyzer comprises a Cassinian trap mass analyzer.

8. A system as recited in claim 6, wherein the electrostatic trapping mass analyzer comprises a trapping region defined by: an inner spindle electrode having an outer surface that is axially symmetric about the longitudinal axis and that is symmetric about a central equatorial plane that is perpendicular to the longitudinal axis; and a pair of outer electrodes disposed at either side of the equatorial plane and having respective inner surfaces, wherein the outer surface of the inner spindle electrode and the inner surfaces of the outer electrodes are shaped such that a trapping potential corresponding to the trapping field is a quadro-logarithmic potential that is established by application of an electrostatic voltage difference between the inner spindle electrode and the outer electrodes.

9. A system as recited in claim 6, wherein the computer readable instructions are further operable to generate a respective mass spectrum from each spectrum of component frequencies by calibrating each spectrum of component frequencies in units of mass-to-charge ratio (m/z).

10. A system as recited in claim 6, wherein each determination of the quality metric by the computer readable instructions is based on one or more of an overall spectral signal-to-noise ratio, a ratio of intensities of two particular spectral peaks and a full-width-at half maximum evaluation of one or more peak widths.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0027] The above noted and various other aspects of the present invention will become apparent from the following description which is given by way of example only and with reference to the accompanying drawings, not drawn to scale, in which:

[0028] FIG. 1A is a schematic depiction of a portion of a mass spectrometer system including an electrostatic trap mass analyzer, specifically an ORBITRAP electrostatic trap mass analyzer;

[0029] FIG. 1B is an enlarged cross sectional view of the electrostatic trap mass analyzer of FIG. 1A;

[0030] FIG. 2A is a depiction of an ideal transient for just a few oscillations of a single frequency component, relating to ions of a particular mass-to-charge (m/z) ratio, as may be measured during operation of the electrostatic trap mass analyzer of FIG. 1A;

[0031] FIG. 2B is a depiction of a simulated transient signal that schematically illustrates the form of an image-current signal and its decay envelope versus time, as may be measured by a Fourier-Transform mass analyzer;

[0032] FIG. 2C is an enlargement of a portion of the simulated transient signal of FIG. 2B between the indicated time points t.sub.1 and t.sub.2;

[0033] FIG. 3A is a set of three experimental measurements of a portion of the mass spectrum of the fungicide pyrimethanil acquired at resolutions of 15000, 30000 and 60000, from top to bottom, respectively;

[0034] FIG. 3B is a set of portions of the mass spectrum of an isotopically labeled sample of adenosine triphosphate (ATP) acquired at resolutions of 15000, 30000, 60000, 120000 and 240000, from top to bottom, respectively;

[0035] FIG. 4 is a flow diagram of a first method, in accordance with the present teachings, of determining a mass spectral resolution setting of a Fourier Transform mass analyzer;

[0036] FIG. 5. is a schematic plot of a partitioned maximum-resolution transient showing a progression of increasing-length transient portions as employed by the method of determining a mass spectral resolution setting of a Fourier Transform mass analyzer that is diagramed in FIG. 4; and

[0037] FIG. 6 is a flow diagram of a second method, in accordance with the present teachings, of determining a mass spectral resolution setting of a Fourier Transform mass analyzer.

DETAILED DESCRIPTION

[0038] The following description is presented to enable any 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 described embodiments will be readily apparent to those skilled in the art and the generic principles herein may be applied to other embodiments. Thus, the present invention is not intended to be limited to the embodiments and examples shown but is to be accorded the widest possible scope in accordance with the features and principles shown and described. The particular features and advantages of the invention will become more apparent with reference to the appended figures taken in conjunction with the following description.

[0039] FIG. 4 is a flow diagram of a first method of determining a mass spectral resolution setting of a Fourier Transform mass analyzer in accordance with the present teachings. In this document the phrase Fourier Transform mass analyzer refers to a type of mass analyzer that generates a transient signal, defined over time, that comprises a superposition of Single Transient Signals, each of which is defined over time and corresponds to a signal of a respective ion species, and from which transient a mass spectrum is calculated using a mathematical transform (generally but not necessarily a Fourier transform) operation. Preferably, the practice of the method 400 employs data acquired from a same sample from which qualitative and/or quantitative analyses of analytes of interest are to be subsequently obtained. In such instances, the illustrated method may comprise a preliminary procedure in preparation for mass spectral analysis of the sample. Additionally, the method may be executed periodically during the course of the mass spectral analysis of the sample, in order to check whether the previously determined resolution remains correct under possibly non-constant experimental conditions, such as changes in the composition of the sample. For example, such composition changes are essentially guaranteed to occur when the sample comprises an effluent stream that is delivered from a liquid or gas chromatograph. Certain steps of the method 400 are better understood with further reference to FIG. 5, which is a schematic plot of a maximum-resolution transient, with the transient signal 31 simply depicted as a shaded area within an envelope 32 in order to avoid a high density of lines. The time point .sub.0 represents the commencement of acquisition of an image current signal at some predetermined time after injection of ions into an electrostatic trap and the remaining timpoints, .sub.1 through .sub.10, represent partition boundaries as described further below.

[0040] The first step, step 401 of the method 400 is acquisition of a transient, as generated by motion of ions of the sample within the mass analyzer, using a maximum resolution setting of the mass analyzer. The maximum resolution of the mass analyzer corresponds to a maximum transient length, measured in units of time. Once acquired, the maximum-resolution transient is partitioned, in step 403, into segments bounded by the time points .sub.0, .sub.1, etc. as indicated in FIG. 5. Although eleven such time points, corresponding to ten transient segments, are depicted in FIG. 5, the method 400 is not limited to any particular number of partitions. The number of partitions employed depends upon the requirements of any particular experimental run, since narrower segments correspond to greater control over the final resolution setting that is determined by execution of the method.

[0041] In step 405 of the method 400, a temporary test transient is extracted from the full-resolution transient by setting the test transient to be just the portion of the transient within the first segment, which is bounded by the time points .sub.0 and .sub.1 and whose transient length, in time units, is indicated by line segment 33 in FIG. 5. In optional step 406, a program variable, denoted here as QUALITY, may be initialized to zero (or to some other value that indicates that the current test transient must undergo a quality evaluation to determine if its spectral resolution is acceptable). This step 406 will generally be executed in cases in which quality is being determined automatically (i.e., algorithmically) by evaluation of a quantitative quality metric, which may be calculated using, determined by or include one or more factors such as mass spectral resolution, an overall signal-to-noise ratio, a ratio of intensities of two particular mass spectral peaks, a full-width-at half maximum evaluation of one or more peak widths, a confidence interval in the accuracy of curve-fitting of overlapping peaks, etc. The calculation of the quality metric may additionally be based on or may include a variety of instrumental and experimental parameters or constraints that are not specific to particular spectrum, such as class of analytes being analyzed or to be analyzed, time available for analysis, etc. and may vary between analyses, between instruments, between analysts or even over the course of a single set of measurements. Alternatively, the step 406 may be skipped in cases in which quality assessments or considerations of resolution appropriateness are being made (step 409) by means of visual inspection of displayed spectra by a human operator or analyst.

[0042] In the next step, step 407 which is part of a possibly-reiterated loop of steps, a frequency spectrum is calculated from the test transient using a mathematical transform operation, such as a Fast-Fourier-Transform (FFT) operation. The calculated frequency spectrum is an uncalibrated representation of a mass spectrum of the sample as would be obtained if the mass analyzer were operated at a resolution setting corresponding to the transient length of the test transient. Since the test transient naturally comprises less information than is available in the full-resolution transient, the resolution of lines in the frequency spectrum is poorer than would be the case if the full-resolution transient signal were transformed. Optionally, the frequency spectrum may be calibrated, in optional step 408, in m/z units if the sample is known to contain or is provided with compounds that yield identifiable lines corresponding to known m/z values or else if instrumental calibration coefficients are already available from a prior calibration.

[0043] Regardless of whether the frequency spectrum obtained from the test transient is calibrated, the features of the spectrum may be examined to determine if the spectrum exhibits appropriate resolution in step 409. As noted above, this determination may be performed automatically if it is based on a quantitative metric that may be evaluated from digital spectral data properties. In such situations, the value of the QUALITY variable is reset to a digital value that reflects the value of the metric, as determined for the most recently calculated frequency spectrum or mass spectrum. Alternatively, a graphical spectral representation of all or a portion of the frequency or mass spectrum and/or of a list of digital metric parameters may be displayed to a human analyst or operator who then makes a simple yes/no decision regarding the whether or not the frequency spectrum exhibits an appropriate resolution or whether or not the resolution-dependent quality is adequate.

[0044] Step 410 of the method 400 is a decision step at which it is decided if spectral resolution should be further improved. The step 410 may be performed according to any of multiple alternative procedures. For instance, if a QUALITY variable is employed to keep track of a digital quality metric, then step 410 may comprise comparing the most-recently-calculated value of the variable to a pre-determined threshold value. Depending upon how the QUALITY variable is defined, an acceptable resolution or quality may either correspond to a value greater than or equal to the pre-determined threshold value (e.g., signal-to-noise ratio) or less than the pre-determined threshold value (e.g., peak width). Alternatively, the decision step 410 may include prompting for and receiving the results of a subjective assessment by a human operator or analyst, either as a keyed-in or graphical-user-interface response.

[0045] Moreover, the term appropriate resolution, as used in regard to steps 409-410 means any resolution that optimizes one or more of the properties of mass spectral resolution, overall signal-to-noise ratio, a ratio of intensities of two particular mass spectral peaks, a full-width-at half maximum evaluation of one or more peak widths, a confidence interval in the accuracy of curve-fitting of overlapping peaks, a confidence assessment of analyte identification and/or analyte concentration, a minimum level of quantitation, a speed of analysis and/or efficiency of instrument operation. Thus, an appropriate resolution is not necessarily (and frequently will not be) a maximum resolution but is, instead, a resolution that provides a best set of results under a particular set of circumstances, with due regard being given to balancing measures of the various properties listed above, as well as possibly others. The level of resolution that constitutes an appropriate resolution in any particular mass spectral analysis may depend on a variety of instrumental and experimental parameters or constraints such as class of analytes, time available for analysis, etc. and may vary between analyses, between instruments, between analysts or even over the course of a single set of measurements.

[0046] The No branch of decision step 410 is followed either if the maximum available resolution has not been reached after execution of a plurality of transient segment appending steps (step 411) or if the frequency spectrum does not exhibit appropriate resolution or an appropriate resolution-dependent level of quality, as discussed above. In such instances, a new test transient signal is constructed in step 411 by appending the data from the next segment of the full-resolution transient onto the greater-time-point end of the prior test transient signal. With reference to FIG. 5, the second test transient would occupy the portion of the full-resolution transient that is bounded by the time points .sub.0 and .sub.2, since the second test transient would be constructed by appending the portion of transient 31 that occupies the region between time points .sub.1 and .sub.2 onto the previous test transient. The second test transient would have a transient length, in time units, is indicated by line segment 34 in FIG. 5.

[0047] From step 411, execution of the method returns to step 407, at which a new frequency spectrum is calculated using the most recent version of the test transient signal. Accordingly, step 409 and possibly step 408 are reiterated using the new frequency spectrum corresponding to the most recently constructed test transient. Because the new test transient naturally comprises more information the prior version of the test transient, the resolution of the new frequency generated by the transform operation is expected to have improved resolution, relative to the prior frequency spectrum. In this fashion, the steps 407, 409 and 411 (and possibly step 408) may be repeated multiple times until the resolution, as determined in step 409, improves to an appropriate level. With reference to FIG. 5, subsequent test transients would correspond, in sequence, to the transient portions corresponding to line segments 35 and 36, and possibly others (not indicated) as the loop of steps is repeated.

[0048] The Yes branch of decision step 410 is followed either if the maximum available resolution has been reached after execution of a plurality of transient segment appending steps (step 411) or if the frequency spectrum has been found or judged to exhibit appropriate resolution or an appropriate resolution-dependent level of quality, as discussed above. In such instances, the transient length for use is subsequent mass spectral data acquisitions is set, at step 413, to the transient length that caused the decision step 410 to follow the Yes branch. Unless the optional procedure 414 is executed, the setting of the transient length is equivalent to setting the instrumental resolution to employed during the subsequent acquisition of mass spectra. Subsequently, in step 415, those mass spectra are acquired, using otherwise normal data acquisition procedures, using the setting determined in the execution of method 400. If desired, these spectra may be monitored for changes (optional step 417), either automatically or by a human operator, that may necessitate re-assessment of appropriate mass spectral resolution that is to be used. Such changes may include, for instance, a change in a signal-to-background signal as may occur if the identity of an analyte of interest changes or of there are changes in a matrix within which an analyte is dispersed. If the changes are deemed to require such a re-assessment, then execution returns to step 401.

[0049] Under some circumstances, it may be desirable to further refine the mass spectral resolution setting after the frequency spectrum has been found or judged, in decision step 410 to exhibit appropriate resolution or an appropriate resolution-dependent level of quality, as discussed above. The acquisition of a transient by an electrostatic trap mass analyzer may consume a significant amount of measurement time which, in some circumstances, may be in short supply. The transient length set in step 413 may provide greater resolution than is necessary and, thus, may consume more instrument time than is necessary. In such cases, the optional resolution adjustment procedure 414 may be executed before mass spectra are acquired. In this procedure, the partition size is reduced and then, the transient (previously set in step 413) is progressively truncated, at its high-time end, by decrements corresponding to the new, smaller partition size. The resolution adjustment procedure 414 is similar to the method 600 that is discussed below in reference to FIG. 6. In brief, each truncation slightly degrades the resolution. The QUALITY value of the resulting calculated frequency spectrum is assessed after each truncation. The process continues until the resolution or QUALITY is no longer acceptable, at which point the transient length is set at its value prior to the most recent truncation. Because the partition size is smaller than that used in the loop of steps 407-411, this optional procedure 414 is capable of more-precisely determining the boundary between adequate and unacceptable mass spectral resolution.

[0050] Method 600 (FIG. 6) is a procedure for determining an appropriate mass spectral resolution from an existing (previously acquired) mass spectrum. The method 600 is suitable when it desired to mass analyze a sample that is similar to the sample from which the previously acquired mass spectrum was obtained, but at a suitably lower mass resolution. For example, the existing mass spectrum may have been acquired at an un-necessarily high resolution. In an initial step 601, an initial test transient may be set equal to the transient that was obtained at the time of the prior measurement, if such a transient is available. Otherwise, if a transient is not available but if a known relationship relating phase, .sub.0 (see Eq. 3), to either frequency, see (Eq. 2) or m/z is available, then steps 602 and 603 may be executed as an alternative to step 601. In step 602, the m/z scale of the mass spectrum is converted to a frequency scale using Eq. 2 and a value of the force constant, k, as determined from one or more prior calibrations. Then, in step 603, a synthetic transient may be calculated using the phase versus m/z relationship, the values determined in step 602 and relative amplitude, A, values taken from the line intensities of the mass spectrum. The synthetic transient is then set as the initial test transient. The length of the calculated initial test transient is set to be equal to the transient length that corresponds to the maximum available mass spectral resolution.

[0051] In optional step 604, a program variable, denoted here as QUALITY, may be initialized to a value Q.sub.hi (or to some other value that indicates that the current test transient must undergo a quality evaluation to determine to what extent the mass spectral resolution may be degraded, relative to that of the previously-acquired mass spectrum, while still remaining acceptable). This step 604 will generally be executed in cases in which quality is being determined automatically (i.e., algorithmically) by evaluation of a quantitative quality metric, such as an overall signal-to-noise ratio, a ratio of intensities of two particular mass spectral peaks, a full-width-at half maximum evaluation of one or more peak widths, a confidence interval in the accuracy of curve-fitting of overlapping peaks, etc. The calculation of the quality metric may additionally be based on or may include a variety of instrumental and experimental parameters or constraints that are not specific to particular spectrum, such as class of analytes being analyzed or to be analyzed, time available for analysis, etc. and may vary between analyses, between instruments, between analysts or even over the course of a single set of measurements. Alternatively, the step 604 may be skipped in cases in which quality assessments or considerations of resolution appropriateness are being made (step 610) by means of visual inspection of displayed spectra by a human operator or analyst.

[0052] Steps 606, 608, 610 and 612 (and possibly step 609) of the method 600 comprise a group of steps that may be re-iterated multiple times. In step 606, the prior test transient is truncated by deleting a portion of that transient at the greater-time end, thereby yielding a new, smaller test transient. For example, with reference to FIG. 5, if the transient 31 is taken as the prior test transient defined over the time range .sub.0 through .sub.10, then the next test transient is generated by deleting the portion of the prior transient between time .sub.9 and time .sub.10, the width of which is the increment by which the transient is shortened. This truncation procedure yields a shorter transient defined over the shorter time range .sub.0 through .sub.9. In step 608, a new test spectrum is calculated (for instance, by means of a Fourier Transform or Fast Fourier Transform procedure) using the most recent truncated test transform. The test spectrum is expected to be a more poorly resolved version of the original mass spectrum, with the resolution decreasing as the test transient becomes shorter.

[0053] The test transient and the truncated test transient are both defined over a time domain. Thus, the test spectrum that is calculated in step 608 is defined over a frequency domain. If desired, the test spectrum may be calibrated in terms of m/z units, in an optional calibration step 609, so as to yield a mass spectrum. The calibration may employ calibration coefficients used in the calibration of the previously-acquired mass spectrum of that corresponds to the previously-acquired transient of step 601.

[0054] Regardless of whether the frequency spectrum obtained from the test transient is calibrated, the features of the spectrum may be examined to determine if the spectrum exhibits adequate quality and/or appropriate resolution in step 610. As noted above, this determination may be performed automatically if it is based on a quantitative metric that may be evaluated from digital spectral data properties. In such situations, the value of the QUALITY variable is reset, in step 610, to a digital value that reflects the value of the metric, as determined for the most recently calculated frequency spectrum (step 608) or mass spectrum (step 609). Alternatively, a graphical spectral representation of all or a portion of the frequency or mass spectrum and/or of a list of digital metric parameters may be displayed to a human analyst or operator who then makes a simple yes/no decision regarding the whether or not the frequency spectrum exhibits an appropriate resolution or whether or not the resolution-dependent quality is adequate.

[0055] Step 612 of the method 600 is a decision step at which it is decided if spectral resolution may be further reduced while still maintaining adequate spectral quality and/or acceptable resolution. If the spectral quality of the test spectrum remains adequate or the resolution of the test spectrum remains appropriate for data acquisition after the most-recent truncation, then execution of the method 600 returns (taking the Yes branch of decision step 612) to step 606 and the transient is further truncated. The step 612 may be performed according to any of multiple alternative procedures. For instance, if a QUALITY variable is employed to keep track of a digital quality metric, then step 612 may comprise comparing the most-recently-calculated value of the variable to a pre-determined threshold value. Depending upon how the QUALITY variable is defined, an acceptable resolution or quality may either correspond to a value greater than or equal to the pre-determined threshold value (e.g., signal-to-noise ratio) or less than the pre-determined threshold value (e.g., peak width). Alternatively, the decision step 612 may include prompting for and receiving the results of a subjective assessment by a human operator or analyst, either as a keyed-in or graphical-user-interface response.

[0056] Moreover, the term appropriate resolution, as used in regard to steps 610-612 means any resolution that optimizes one or more of the properties of mass spectral resolution, overall signal-to-noise ratio, a ratio of intensities of two particular mass spectral peaks, a full-width-at half maximum evaluation of one or more peak widths, a confidence interval in the accuracy of curve-fitting of overlapping peaks, a confidence assessment of analyte identification and/or analyte concentration, a minimum level of quantitation, a speed of analysis and/or efficiency of instrument operation. Thus, an appropriate resolution is not necessarily (and frequently will not be) a maximum resolution but is, instead, a resolution that provides a best set of results under a particular set of circumstances, with due regard being given to balancing measures of the various properties listed above, as well as possibly others. The level of resolution that constitutes an appropriate resolution in any particular mass spectral analysis may depend on a variety of instrumental and experimental parameters or constraints such as class of analytes, time available for analysis, etc. and may vary between analyses, between instruments, between analysts or even over the course of a single set of measurements.

[0057] Looping through steps 606-612 of the method 600 continues until either the mass spectral resolution is determined, in step 612, to be no longer appropriate for planned subsequent mass spectral data acquisition or else the length of the test transient has been truncated to shorter than a pre-determined minimum length. In such circumstances, the transient has been truncated one time too many. Therefore, execution of the method 600 proceeds to step 613, at which the transient length to be employed for subsequent mass spectral data acquisition is set to be equal to the length of the test transient prior to most recent truncation. Provided that optional procedure 614 is not executed, this setting of the transient length is equivalent to setting a mass spectral resolution to be used during the for subsequent mass spectral data acquisition. Finally, the mass spectra are acquired in step 615.

[0058] Under some circumstances, it may be desirable to further refine the mass spectral resolution setting after the No branch of decision step 612 has been followed. In such circumstance, step 613 is bypassed and the resolution adjustment procedure 614 is executed instead. The procedure 614 is similar to the method 400 that has been discussed above in reference to FIG. 4. Because step 613 is bypassed, the test transient at the beginning of procedure 614 does not yield acceptable quality or resolution. Therefore, in the resolution adjustment procedure 614, the test transient length is progressively increased, in increments corresponding to a new, smaller partition size. Each increase slightly improves the resolution and the QUALITY value of the resulting calculated test spectrum is assessed at each step. The process continues until the resolution or QUALITY is acceptable.

[0059] Improved methods for setting a mass spectral resolution to be employed during operation of a Fourier Transform mass spectrometer have been herein disclosed. Various methods taught herein are advantageous in that there is no requirement for the needed experimental resolution to be known in advance by a human operator or analyst and that the resolution, and consequently the spectral acquisition rate, can be changed as needed in real time (while the spectra are being acquired) based on properties of the acquired spectra, such as the levels of the background and analyte signals, the appearance of new lines in the spectra, or the disappearance of previously observed lines from the spectra. The ability to change resolution and spectral acquisition rate in such a data dependent fashion can potentially improve the efficiency of data collection, especially when the spectra are changing with time as a result of the inlet sample stream comprising chromatographic sample fractions that are separated by either liquid or gas chromatography.

[0060] The discussion included in this application is intended to serve as a basic description. Although the invention has been described in accordance with the various embodiments shown and described, one of ordinary skill in the art will readily recognize that there could be variations to the embodiments and those variations would be within the spirit and scope of the present invention. The reader should be aware that the specific discussion may not explicitly describe all embodiments possible; many alternatives are implicit. Accordingly, many modifications may be made by one of ordinary skill in the art without departing from the scope and essence of the invention. Neither the description nor the terminology is intended to limit the scope of the invention. Any patents, patent applications, patent application publications or other literature mentioned herein are hereby incorporated by reference herein in their respective entirety as if fully set forth herein.