Method for determining a parameter to perform a mass analysis of sample ions with an ion trapping mass analyser

Abstract

A method for determining a compensation factor parameter, c, for controlling an amount of ions ionised that are injected from an ion storage unit into mass analyser, where c is an adjustment factor that is applied to optimized injection times that are based on an optimized visible charge of a reference sample, the method comprising: detecting at least one mass spectrum for at least one amount of injected ions; determining from the at least one detected mass spectrum, a slope, s(sample), of a linear correlation of a relative m/z shift with visible total charge Q.sub.v of detected mass spectra; determining the compensation factor c as c=s(reference)/s(sample) where s(reference) is the slope of a linear correlation between reference-sample relative m/z shift values and reference-sample visible charge values determined from a plurality of mass spectra detected from a plurality of respective pre-selected amounts of a clean reference sample.

Claims

1. A method for determining a parameter for controlling an amount of sample ions ionised from a sample, which is injected from an ion storage unit into an ion trapping mass analyser to perform a mass analysis of the sample ions comprising the steps: detecting mass spectra for different amounts of the sample ions injected from the ion storage unit with the ion trapping mass analyser; evaluating the observable difference of a relative m/z shift from the detected mass spectra of at least two of the different amounts of the sample ions induced by a space charge of the sample ions by determination of the relative difference of m/z values of at least one species of sample ions from these detected mass spectra; evaluating a visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v from the detected mass spectra of the at least two of the different amounts of the sample ions; determining from the evaluated observable differences of the relative m/z shift and the evaluated visible total charges Q.sub.v and/or the differences of the visible total charge Q.sub.v the sample slope of a linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser; and determining a compensation factor c to adjust an ion injection time period t.sub.opt,v of sample ions into the ion storage unit, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample, to perform a mass analysis of sample ions, wherein the ion injection time period t.sub.opt,v is determined from the visible total charge Q.sub.v evaluated from at least one mass spectrum of at least one amount of the sample ions detected with the ion trapping mass analyser and the corresponding injection time period of the sample ions, by dividing the reference slope of a linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of reference ions ionised from the reference sample detected with the ion trapping mass analyser by the determined sample slope.

2. The method of claim 1, wherein the observable difference of the relative m/z shift is evaluated from the detected mass spectra by determination of the relative difference of m/z values of at least 3 species of sample ions from these detected mass spectra.

3. The method of claim 2, wherein the observable difference of the relative m/z shift is evaluated from the detected mass spectra by determination of the relative difference of m/z values of at least 3 species of sample ions from these detected mass spectra.

4. The method of claim 1, wherein the observable difference of a relative m/z shift is evaluated from the detected mass spectra by determination of the relative difference of m/z values of species of sample ions from these detected mass spectra, wherein these species of sample ions have a signal-to-noise ratio in the detected mass spectra greater than 5.

5. The method of claim 2, wherein the observable difference of a relative m/z shift is evaluated from the detected mass spectra by determination of the relative difference of m/z values of species of sample ions from these detected mass spectra, wherein these species of sample ions have a signal-to-noise ratio in the detected mass spectra greater than 5.

6. The method of claim 1, wherein the reference sample is a clean sample.

7. The method of claim 1, wherein the ion trapping mass analyser is a Fourier transform mass analyser.

8. The method of claim 1, wherein the compensation factor c is determined by repeated determination of compensation factor values and averaging over the time.

9. The method of claim 1, wherein the sample slope is determined from the mass spectra detected for two pre-selected amounts of the sample ions.

10. The method of claim 1, wherein the sample slope is determined from the mass spectra detected for the different amounts of the sample ions by using a linear fit.

11. A method for determining a parameter for controlling an amount of sample ions ionised from a sample, which is injected from an ion storage unit into an ion trapping mass analyser to perform a mass analysis of the sample ions, wherein the m/z ratio of at least one of the sample ions is known, comprising the steps: detecting at least one mass spectrum for at least one amount of the sample ions injected from the ion storage unit with the ion trapping mass analyser; evaluating the relative m/z shift from the at least one detected mass spectrum of the at least one amount of the sample ions induced by a space charge of the sample ions by determination of a relative difference of m/z values of at least one sample ion, for which the m/z ratio is known, in the at least one detected mass spectrum to its known m/z ratio; evaluating a visible total charge Q.sub.v from the at least one detected mass spectrum of the at least one amount of the sample ions; determining, from the evaluated relative m/z shift value or values and the evaluated visible total charge or charges Q.sub.v the sample slope of a linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser; and determining a compensation factor c to adjust the ion injection time period t.sub.optv of sample ions into the ion storage unit, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample, to perform a mass analysis of sample ions, wherein the ion injection time period t.sub.optv is determined from the visible total charge Q.sub.v evaluated from at least one mass spectrum of at least one amount of the sample ions detected with the ion trapping mass analyser and the corresponding injection time period of the sample ions, by dividing the reference slope of a linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of reference ions ionised from the reference sample detected with the ion trapping mass analyser by the determined sample slope.

12. The method of claim 11, wherein the reference sample is a clean sample.

13. The method of claim 11, wherein the ion trapping mass analyser is a Fourier transform mass analyser.

14. The method of claim 11, wherein the compensation factor c is determined by repeated determination of compensation factor values and averaging over the time.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 shows an embodiment of a Fourier transform mass spectrometer in which the invention can be applied.

(2) FIG. 2A shows the correlation of the visible total charge of an ion package with the injection time period of the ions into an ion storage unit for a sample which shall be analysed and a clean sample.

(3) FIG. 2B shows the correlation of the visible total charge of an ion package with the injection time period of the ions into an ion storage unit for a sample which shall be analysed and a reference sample.

(4) FIG. 2C shows the correlation of the visible total charge of an ion package with the injection time period of the ions into an ion storage unit for a sample comprising a standard component which shall be analysed and a reference sample.

(5) FIG. 3 shows an example of a mass spectrum with several mass peaks.

(6) FIG. 4 shows another example of a mass spectrum with several mass peaks.

(7) FIG. 5A shows the correlation of the relative m/z shift in a mass spectrum of an ion package with the visible total charge of an ion package for a sample which shall be analysed and a clean sample.

(8) FIG. 5B shows the correlation of the relative m/z shift in a mass spectrum of an ion package with the visible total charge of an ion package for a sample which shall be analysed and a reference sample.

(9) FIG. 5C shows the correlation of the relative m/z shift in a mass spectrum of an ion package with the visible total charge of an ion package for a sample comprising a standard component which shall be analysed and a reference sample.

(10) FIG. 6 shows the flow chart of the inventive method of claim 2 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into an ion trapping mass analyser.

(11) FIG. 7 shows the mass spectra of sample ions of different pre-selected amounts of sample ions.

(12) FIG. 8 shows the flow chart of an embodiment of the inventive method of claim 9 for performing a mass analysis of sample ions in an ion trapping transform mass analyser.

(13) FIG. 9 shows the flow chart of the inventive method of claim 5 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into an ion trapping mass analyser, wherein the m/z ratio of at least one of the sample ions is known.

(14) FIG. 10 shows the flow chart of another embodiment of the inventive method of claim 9 for performing a mass analysis of sample ions in an ion trapping transform mass analyser, wherein the m/z ratio of at least one of the sample ions is known.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

(15) FIG. 1 shows an embodiment of a Fourier transform mass spectrometer 2 in which sample ions are generated from a sample in an ion source (not shown), which may be a conventional ion source such as an electrospray ionisation ion source. Sample ions may be generated as a continuous stream in the ion source as in an electrospray ionisation ion source, or in a pulsed manner as in a MALDI source. The sample which is ionised in the ion source may come from an interfaced instrument such as a liquid chromatograph (not shown). The ions pass through a heated capillary 4 (typically held at 320° C.), are transferred by an RF only S-lens 6 (RF amplitude 0-350 Vpp, being set mass dependent), and pass the S-lens exit lens 8 (typically held at 25V). The ions in the ion beam are next transmitted through an injection flatapole 10 and a bent flatapole 12 which are RF only devices to transmit the sample ions. The sample ions then pass through a pair of lenses (with inner lens 14 typically at about 4.5V, and outer lens 16 typically at about −100V) and enter a mass resolving quadrupole 18.

(16) The quadrupole 18 DC offset is typically 4.5 V. The differential RF and DC voltages of the quadrupole 18 are controlled to either transmit a wide mass range of sample ions (RF only mode) or select sample ions of particular m/z for transmission by applying RF and DC according to the Mathieu stability diagram. It will be appreciated that, in other embodiments, instead of the mass resolving quadrupole 18, an RF only quadrupole or multipole may be used as an ion guide but the spectrometer would lack the capability of mass selection before analysis. In still other embodiments, an alternative mass resolving device may be employed instead of quadrupole 18, such as a linear ion trap, magnetic sector or a time-of-flight analyser. Such a mass resolving device could be used for mass selection and/or ion fragmentation. Turning back to the shown embodiment, the ion beam which is transmitted through quadrupole 18 exits from the quadrupole through a quadrupole exit lens 20 (typically held at −35 to 0V, the voltage being set mass dependent) and is switched on and off by a split lens 22. Then the ions are transferred through a transfer multipole 24 (RF only, RF amplitude being set mass dependent) and collected in an ion storage unit, a curved linear ion trap (C-trap) 26. The C-trap is elongated in an axial direction (thereby defining a trap axis) in which the sample ions enter the trap. Voltage on the C-trap exit lens 28 can be set in such a way that sample ions cannot pass and thereby get stored within the C-trap 26. Similarly, after the desired ion injection time period, which is also the ion accumulation time (or number of ion pulses e.g. with MALDI) into the C-trap has been reached, the voltage on C-trap entrance lens 30 is set such that sample ions cannot pass out of the trap and sample ions are no longer injected into the C-trap. More accurate gating of the incoming ion beam is provided by the split lens 22. The sample ions are trapped radially in the C-trap by applying RF voltage to the curved rods of the trap in a known manner.

(17) Sample ions which are stored within the C-trap 26 can be ejected orthogonally to the axis of the trap (orthogonal ejection) by pulsing DC to the C-trap in order for the sample ions to be injected, in this case via Z-lens 32, and deflector 33 into a Fourier transform mass analyser 34, which in this case is an electrostatic orbital trap, and more specifically an Orbitrap™ FT mass analyser made by Thermo Fisher Scientific Inc. The orbital trap 34 comprises an inner electrode 40 elongated along the orbital trap axis and a split pair of outer electrodes 42, 44 which surround the inner electrode 40 and define there between a trapping volume in which ions are trapped and oscillate by orbiting around the inner electrode 40 to which is applied a trapping voltage whilst oscillating back and forth along the axis of the trap. The pair of outer electrodes 42, 44 function as detection electrodes to detect an image current induced by the oscillation of the ions in the trapping volume and thereby provide a detected signal. The outer electrodes 42, 44 thus constitute a first detector of the system. The outer electrodes 42, 44 typically function as a differential pair of detection electrodes and are coupled to respective inputs of a differential amplifier (not shown), which in turn forms part of a digital data acquisition system (not shown) to receive the detected signal. The detected signal can be processed using Fourier transformation to obtain a mass spectrum. The digital data acquisition system can be a part of or connected with a control unit of the mass spectrometer 2.

(18) The control unit may comprise one or processors to process the detected signal using e.g. Fourier transformation and/or to generate a mass spectrum. The control unit is configured or programmed to execute at least one of the methods of the invention. The control unit may comprise an instrument interface, which is adapted to send commands to or operate the mass spectrometer. The control unit may comprise a storage unit for storing data in data sets. Connection between the control unit and the spectrometer may be established by a wire or a glass fibre or wirelessly via radio communication. Preferably, the control unit further comprises visualization means, in particular a display and/or a printer, and interaction means, in particular a keyboard and/or a mouse, so that a user can view and enter information. When the control unit comprises visualization means and interaction means, operation of the spectrometer is preferably controlled via a graphical user interface (GUI). The control unit can be realized as a standard personal computer or in a distributed form with a number of processing devices interconnected by a wired or wireless network.

(19) The mass spectrometer 2 further comprises a collision or reaction cell 50 downstream of the C-trap 26. Sample ions collected in the C-trap 26 can be ejected orthogonally as a pulse to the mass analyser 34 without entering the collision or reaction cell 50 or the sample ions can be transmitted axially to the collision or reaction cell for processing before returning the processed sample ions to the C-trap for subsequent orthogonal ejection to the mass analyser. The C-trap exit lens 28 in that case is set to allow sample ions to enter the collision or reaction cell 50 and sample ions can be injected into the collision or reaction cell by an appropriate voltage gradient between the C-trap and the collision or reaction cell (e.g. the collision or reaction cell may be offset to negative potential for positive sample ions). The collision energy can be controlled by this voltage gradient. The collision or reaction cell 50 comprises a multipole 52 to contain the sample ions. The collision or reaction cell 50, for example, may be pressurised with a collision gas so as to enable fragmentation (collision induced dissociation) of sample ions therein, or may contain a source of reactive ions for electron transfer dissociation (ETD) of sample ions therein. The ions are prevented from leaving the collision or reaction cell 50 axially by setting an appropriate voltage to a collision cell exit lens 54. The C-trap exit lens 28 at the other end of the collision or reaction cell 50 also acts as an entrance lens to the collision or reaction cell 50 and can be set to prevent ions leaving whilst they undergo processing in the collision or reaction cell if need be. In other embodiments, the collision or reaction cell 50 may have its own separate entrance lens. After processing in the collision or reaction cell 50 the potential of the cell 50 may be offset so as to eject processed sample ions back into the C-trap (the C-trap exit lens 28 being set to allow the return of the ions to the C-trap) for storage, for example the voltage offset of the cell 50 may be lifted to eject positive charged processed sample ions back to the C-trap. The processed sample ions thus stored in the C-trap may then be injected into the mass analyser 34 as described before. For clarity, processed sample ions are sample ions, because they are in a first step ionised from the investigated sample.

(20) It will be appreciated that the path of the ion beam of sample ions through the spectrometer and in the mass analyser is under appropriate evacuated conditions as known in the art, with different levels of vacuum appropriate for different parts of the spectrometer.

(21) The mass spectrometer 2 is under the control of a control unit, such as an appropriately programmed computer (not shown), which controls the operation of various components and, for example, sets the voltages to be applied to the various components and which receives and processes data from various components including the detectors. The computer is configured to use an algorithm, e.g. contained in a computer program, in accordance with the present invention to determine the settings (e.g. injection time periods or number of ion pulses, amounts of ions, compensation factor c, sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v in the mass spectra) for the injection of sample ions into the C-trap for analytical scans in order to achieve the desired sample ion content (i.e. number of sample ions) therein which avoids space charge effects whilst optimising the statistics of the collected data from the analytical scan. Preferably the computer is also configured to use an algorithm in accordance with the present invention to correct the m/z shift of mass spectra.

(22) The inventive methods of the claims 1, 2 and 5 are determining a parameter for controlling the amount of sample ions, which are injected into an ion trapping mass analyser, in particular into a Fourier transform mass analyser, e.g. the Orbitrap™ FT mass analyser of the Fourier transform mass spectrometer shown in FIG. 1, for which a mass analysis shall be performed in the Fourier transform mass analyser. These sample ions are injected in a very short time period of typically 0.03 milliseconds to 300 milliseconds from the ion storage unit into the Fourier transform mass analyser. In the Fourier transform mass spectrometer shown in FIG. 1 the stored sample ions within the C-trap 26 are ejected orthogonally to the axis of the trap (orthogonal ejection) by pulsing DC to the C-trap in order for the sample ions to be injected via Z-lens 32 and deflector 33 into the Orbitrap™ FT mass analyser 34.

(23) The amount of sample ions stored in the ion storage unit, which in the embodiment of FIG. 1 is the C-trap, is defined by the injection time period t.sub.inj, also termed ion accumulation or fill time, in which sample ions flow into the ion storage unit, normally with a constant or nearly constant total ion current TIC (constant over time). Instead of the constant total ion current TIC sample ions can be also supplied by a number of sample ion pulses during the injection time period t.sub.inj into the ion storage unit.

(24) In FIG. 2A is shown the correlation between the visible total charge Q.sub.v of the ion package stored in the ion storage unit and the injection time period, i.e. accumulation time, t.sub.inj of the ions, i.e. time taken to accumulate ions in the ion storage unit. The visible total charge Q.sub.v of the ions can be derived from a mass spectrum detected by the ion trapping mass analyser to which the ion package is injected from the ion storage unit as explained before. The correlation is shown for the ion packages of two different samples injected into the ion storage unit with the same total ion current TIC, which is taking into account the real, i. e. actual, total charge of the ions Q.sub.real. The correlation 100 shows the correlation when the real (i.e. actual) total charge Q.sub.real of the ion package of a clean sample is visible in a detected mass spectrum, so that Q.sub.v=Q.sub.real. Due to a constant total ion current TIC of ions from the ion source the correlation is provided by a linear function, a straight line. When a prescan 130 is executed as explained above with the injection time period of the prescan t.sub.pre and the visible charge Q.sub.v,pre (=Q.sub.real,pre) is determined from the mass spectrum of the prescan 130, the optimised accumulation time t.sub.opt,real can be determined for an optimised total charge Q.sub.opt of the ion trapping mass analyser by the formula (1) described before:

(25) 0$\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=\frac{Q_{opt}}{Q_{v,\mathrm{pre}}}\times t_{pre}& \left(14\right)\end{array}$

(26) The second correlation 120 shows the correlation of the injection time period t.sub.inj and the visible total charge Q.sub.v, when the real total charge Q.sub.real of the ion package of the sample ions of a sample, which shall be analysed, is not completely visible in a detected mass spectrum, so that Q.sub.v<Q.sub.real. If now the injection time period would be optimised according the formula mentioned before, the reduced amount of the visible total charge Q.sub.v would result in an increased optimised injection time period t.sub.opt,v which would be related to the value Q.sub.v=Q.sub.opt, because it is determined from the visible total charge Q.sub.v evaluated from detected mass spectra. Therefore another method is required to define an optimised accumulation time t.sub.opt,real when the complete total charge Q.sub.real of an ion package of sample ions is not visible in its detected mass spectrum.

(27) In the mass spectra shown in the FIGS. 3 and 4 it is schematically explained why sometimes the charge of sample ions is not visible in their detected mass spectrum.

(28) In the mass spectrum of FIG. 3 are shown 4 mass peaks 200, 210, 220 and 230 of sample ions having different m/z values. The peaks 200 and 210 are separated from each other and therefore their full intensity is used to calculate the visible total charge Q.sub.v of the analysed ion package. The mass peaks 220 and 230 are interfering and therefore their separate intensity is reduced, when the peaks are convoluted. Therefore the visible total charge Q.sub.v of the sample ions of these peaks is lowered in comparison to their real charge Q.sub.real.

(29) In the mass spectrum of FIG. 4 are shown 3 large mass peaks 300, 310, and 320 of sample ions having a signal-to-noise ratio of a level above a threshold that they are taken into account to determine the visible total charge Q.sub.v of the mass spectrum. Other mass peaks 330 and 340 of sample ions are superposed by the larger peaks and therefore not taken into account to determine the visible total charge Q.sub.v of the investigated sample ions from the mass spectrum. Also the very small peaks 350 and 360, which are related to specific sample ions of low abundance in the ion package, are not taken into account to determine the visible charge Q.sub.v of the sample ions form the mass spectrum because their signal-to-noise ratio is too low. So the visible total charge Q.sub.v (solid line) evaluated from the mass spectrum is below the real total charge Q.sub.real of the investigated ion package of the sample ions, because there are invisible charges shown by the dashed line.

(30) To solve the problem to determine the optimised injection time period t.sub.opt,real, when not all charges are visible in a mass spectrum, the invention uses the effect that the relative m/z shift of the mass peaks in a mass spectrum induced by the space charge of the ion package of sample ions is related to the real total charge Q.sub.real of an ion package of the sample ions, wherein the relative m/z shift of the mass peaks is proportional to the real total charge Q.sub.real.

(31) $\begin{array}{cc}\frac{\Delta m\text{/}z}{m\text{/}z}\propto Q_{\mathrm{real}}& \left(15\right)\end{array}$

(32) In FIG. 5A is shown the correlation of the relative m/z shift of the mass peaks of a mass spectrum of an ion package detected with an ion trapping mass analyser with the visible total charge Q.sub.v of the ion package derived from its detected mass spectrum.

(33) The first correlation 400 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of mass spectra of a clean sample, when the real total charge Q.sub.real of the ion package of clean sample ions is visible in a detected mass spectrum. This correlation 400 is provided by a linear function, a straight line. The slope of this function, the clean sample slope is a standard value, which is only related to the type of the particular used ion trapping mass analyser and defined by the geometry and the electromagnetic fields of the specific mass analyser type. In FIG. 5A is also shown optimised total charge Q.sub.opt of the ion trapping mass analyser on the horizontal axis showing the visible total charge Q.sub.v. Therefore it can be deduced from the first correlation 400 the relative m/z shift of a mass spectrum, when an ion package of the optimised total charge Q.sub.opt is analysed in the ion trapping mass analyser, the relative m/z shift at the optimised total charge Q.sub.opt, having the value:

(34) $\begin{array}{cc}{\left(\frac{\Delta m\text{/}z}{m\text{/}z}\right)}_{opt}& \left(16\right)\end{array}$

(35) The second correlation 420 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of a sample, which shall be analysed, when the total charge Q.sub.real of the ion package of the sample ions is only partially visible in a detected mass spectrum. Also, this correlation 420 is assumed by a linear function, a straight line. But the function has a greater slope, because the visible total charge Q.sub.v of the sample ions which can be derived from a mass spectrum is reduced.

(36) It should be emphasised that the values of the relative m/z values and visible total charge Q.sub.v observed for specific measured mass spectra may deviate from this linear correlation due to measurement errors and higher-order physical effects. This has to be taken into account when the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the sample is determined. Therefore it is advantageous to use at least three different amounts of sample ions, preferably to use more than five different amounts of sample ions and particular preferably to use more than 10 different amounts of sample ions to determine from their mass spectra the sample slope of the linear correlation. In preferred embodiments then the sample slope is determined by using a linear fit or averaging method, as described in detail before. The sample slope can be determined e.g. by averaging the ratio of the relative m/z shift to the visible total charge Q.sub.v of the different amounts of sample ions, when the m/z ratio of at least one of the sample ions is known in a method of claim 5, or the ratio of the difference of the relative m/z shift and the difference of the visible total charge Q.sub.v of different pairs of the different amounts of sample ions, when the m/z ratio of at least one of the sample ions is known in a method of claim 5. The sample slope can be determined in a method of claim 2 e.g. by averaging the ratio of the observable difference of the relative m/z shift to the difference of the visible total charge Q.sub.v determined from detected mass spectra of different pairs of the different amounts of sample ions.

(37) For the relative m/z shift at the optimised total charge Q.sub.opt

(38) $\begin{array}{cc}{\left(\frac{\Delta m\text{/}z}{m\text{/}z}\right)}_{opt}& \left(17\right)\end{array}$
the visible total charge Q.sub.v,opt can be determined. When this visible total charge Q.sub.v,opt is derived from a mass spectrum of the sample ions, described by the correlation 420, the investigated ion package of the sample ions is actually comprising the optimised real total charge Q.sub.opt.

(39) Therefore, when the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, the accumulation time t.sub.opt,real to detect the ion package of the optimised total charge Q.sub.opt, which is accordingly related to the optimised visible charge of the clean sample Q.sub.clean,opt=Q.sub.opt, can be derived from the total ion current of the visible charge TIC.sub.v shown by the second correlation 120 in FIG. 2A:

(40) $\begin{array}{cc}TI{C}_v=\frac{Q_{opt}}{t_{\mathrm{opt},v}}=\frac{Q_{v,\mathrm{opt}}}{t_{\mathrm{opt},\mathrm{real}}}& \left(18\right)\end{array}$

(41) So the optimised ion injection time period, which is the optimised accumulation time, t.sub.opt,real of sample ions, whose real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, is correlated with the ion injection time period t.sub.opt,v of the sample ions into the ion storage unit to perform a mass analysis of sample ions, when the visible total charge Q.sub.v of the sample ions has the value of the optimised real total charge Q.sub.opt, determined from the visible total charge Q.sub.v in the detected mass spectra of the sample ions:

(42) $\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=\frac{Q_{v,\mathrm{opt}}}{Q_{opt}}{t}_{\mathrm{opt},v}& \left(19\right)\end{array}$
The ratio Q.sub.v,opt/Q.sub.opt can be derived from the correlations in FIG. 5A taking into account the clean slope s(clean) of the correlation 400 of a clean sample and the sample slope s(sample) of the correlation 420 of the sample, for which the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum.

(43) $\begin{array}{cc}\frac{Q_{v,\mathrm{opt}}}{Q_{opt}}=\frac{s\left(\mathrm{clean}\right)}{s\left(\mathrm{sample}\right)}& \left(20\right)\end{array}$
The inventive method is now using this correlation and is determining the correlation factor c:

(44) $\begin{array}{cc}c=\frac{Q_{v,\mathrm{opt}}}{Q_{opt}}=\frac{s\left(\mathrm{clean}\right)}{s\left(\mathrm{sample}\right)}& \left(21\right)\end{array}$
So the correlation factor c is determined by dividing the clean slope s(clean) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the clean sample detected with the ion trapping mass analyser by the sample slope s(sample) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the sample detected with the ion trapping mass analyser.

(45) Then the optimised accumulation time t.sub.opt,real of sample ions, whose real total charge Q.sub.real of their ion package of ions is only partially visible in a detected mass spectrum, is correlated with the ion injection time period t.sub.opt,v of sample ions in the ion storage unit determined from their visible total charge Q.sub.v, as described above:
t.sub.opt,real=ct.sub.opt,v  (22)

(46) The clean slope s(clean) of the correlation 400 of a clean sample is a standard value, which is only related to the type of used ion trapping mass analyser. The clean slope s(clean) is the standard ratio of the type of used ion trapping mass analyser of the relative m/z shift to the visible total charge Q.sub.v,cl of a mass spectrum of clean sample ions and of the difference of the relative m/z shift to the difference of the visible total charge Q.sub.v,cl of two mass spectra of two amounts of clean sample ions trapped in the ion trapping mass analyser and can be determined by a calibration process of the ion trapping transform mass analyser. These values can be determined directly from the mass spectra detected during the calibration process, when at least for one of the clean sample ions the m/z ratio is known. Then the clean slope is determined in the same way as the sample slope in the method of the claim 5. It can be sufficient to determine by the calibration process the slope of the type of used ion trapping mass analyser by executing the calibration process only for one or a few instruments. Preferably the standard value of the slope of the type of used ion trapping mass analyser is determined by averaging the clean slope s(clean) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v,cl of the mass spectra of clean sample ions determined for a few instruments. As usual the clean slope s(clean) can be determined from test measurements (pre-experiments) of clean samples defining the correlation 400. In particular the clean slope s(clean) can be determined using a linear fit, which is applied to the correlation 400 defined by the test measurements (pre-experiments). The clean slope s(clean) of the ion trapping mass analyser can be also provided by a theoretical approach describing the m/z shift in the ion trapping mass analyser and its dependency on the total charge Q.sub.real of an investigated ion package of the clean sample ions.

(47) If no sample ion of the clean sample has a known m/z value, if would be also possible to determine the clean slope of the clean sample according to the approach of the method of claim 2 to determine a sample slope. Then mass spectra of different amounts of clean sample ions have to be detected and from these mass spectra the observable difference of a relative m/z shift has to be evaluated from the detected mass spectra of at least two of the different amounts of the clean sample ions by determination of the relative difference of m/z values of at least one species of clean sample ions from these detected mass spectra. Additional the visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v has to be evaluated from the detected mass spectra of the at least two of the different amounts of the clean sample ions. Then the clean slope can be determined from the evaluated observable difference of the relative m/z shift and the evaluated values of the visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v as explained in detail before for the determination of the sample slope. Because many different samples are known as clean samples and accordingly for at least of their sample ions its m/z ratio is known, this approach to determine the clean slope is only sometimes used.

(48) The sample slope s(sample) of the correlation 420 of the sample, for which real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, can be determined by prescans of different amounts of the investigated sample ions in the ion trapping mass analyser.

(49) In FIG. 5A the sample slope s(sample) is determined by two pre-experiments prescan1, and prescan2, in which for two different amounts of sample ions a mass spectrum is detected in the ion trapping mass analyser. The ion injection time period of the investigated sample ions in the ion storage unit of these prescans is shown in FIG. 2A. The prescan1 is shown by the circle 160 having an ion injection time period t.sub.pre1 and the prescan2 is shown by the circle 170 having an ion injection time period t.sub.pre2. The parameters of prescan1 are shown in FIG. 5A by the circle 430 and the parameters of prescan2 are shown in FIG. 5A by the circle 440.

(50) In this embodiment the sample slope s(sample) is evaluated by the steps: Evaluation of the observable difference of a relative m/z shift from the detected mass spectra of prescan1 and prescan2 by determination of the relative difference of m/z values of at least one species of samples ions from the mass spectra of prescan1 and prescan2 Evaluation the difference of a visible total charge Q.sub.v from the detected mass spectra of prescan1 and prescan2 of the amounts of sample ions trapped in the ion trapping mass analyser Determination of the sample slope s(sample) by calculating the ratio of the evaluated observable difference of the relative m/z shift of the mass spectra of prescan1 and prescan2 and the evaluated difference of the visible total charge Q.sub.v of the mass spectra of prescan1 and prescan2.

(51) This approach to determine the sample slope and is used in the inventive method of claim 2 and can be used in the inventive method of claim 1 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into a ion trapping mass analyser to perform a mass analysis of sample ions, which enables a mass analysis with ion packages of samples ions of the optimised total charge Q.sub.opt, when the real total charge Q.sub.real of an ion package of sample ions is not visible in and/or derivable from a detected mass spectrum. The method relies only on the measurements of mass spectra with the ion trapping mass analyser and the AGC approach to derive the visible total charge Q.sub.v from the detected mass spectra. Other charge detection is not required in the ion trapping mass spectrometer.

(52) In FIG. 2B is shown the correlation between the visible total charge Q.sub.v of the ion package stored in the ion storage unit and the injection, i.e. accumulation, time t.sub.inj of the ions, i.e. time taken to accumulate ions in the ion storage unit. The visible total charge Q.sub.v can be derived from a mass spectrum detected by the ion trapping mass analyser to which the ion package is injected from the ion storage unit as explained before. The correlation is shown for the ion packages of two different samples injected into the ion storage unit with the same total ion current TIC, which is taking into account the real total charge of the ions Q.sub.real. The correlation 180 shows the correlation when the complete real total charge Q.sub.real of the ion package of reference ions of a reference sample is only partially visible as visible total charge Q.sub.v,ref in a detected mass spectrum, so that Q.sub.v,ref<Q.sub.real. Due to a constant total ion current TIC of reference ions from the ion source the correlation is provided by a linear function, a straight line. When a prescan 182 is executed as explained above with the injection time period of the prescan t.sub.pre and the visible charge Q.sub.v,pre determined from the mass spectrum of the prescan 182, the optimised accumulation time t.sub.opt,ref of reference ions can be determined for an optimised total charge Q.sub.ref,opt of the reference ions of the ion trapping mass analyser by the formula already described before:

(53) $\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=t_{\mathrm{opt},\mathrm{ref}}=\frac{Q_{ref,opt}}{Q_{v,pre}}{t}_{pre}& \left(23\right)\end{array}$

(54) The second correlation 120 shows the correlation of the injection time period t.sub.inj and the visible total charge Q.sub.v, when the real total charge Q.sub.real of the ion package of sample ions of a sample, which shall be analysed, is not completely visible in a detected mass spectrum, so that Q.sub.v<Q.sub.real. Further the visible total charge Q.sub.v of the sample ions, which shall be analysed, is smaller than visible total charge Q.sub.v,ref of the reference ions, so that Q.sub.v<Q.sub.v,ref<Q.sub.real. If now the injection time period would be optimised according the formula mentioned before, the reduced amount of the visible total charge Q.sub.v would result in an increased injection time period t.sub.opt,v, which is related to the optimised visible charge Q.sub.opt,ref of the reference sample, because it is determined from the visible total charge Q.sub.v evaluated from detected mass spectra of sample ions. Therefore another method is required to define an optimised accumulation time t.sub.opt,real when the visible total charge Q.sub.v,ref of an ion package of a reference sample is not completely visible in detected mass spectrum of a sample, which shall be investigated.

(55) It should be noted, that it is also possible, that the visible total charge Q.sub.v of the sample ions can be larger than the visible total charge Q.sub.v,ref of the reference ions.

(56) To solve the problem to determine the optimised injection time period t.sub.opt,real, when not all charges are visible in a mass spectrum, the invention uses the effect that the relative m/z shift of the mass peaks in a mass spectrum induced by the space charge of the ion package is related to the real charge Q.sub.real of an ion package, wherein the relative m/z shift of the mass peaks is proportional to the real charge Q.sub.real.

(57) $\begin{array}{cc}\frac{\Delta m\text{/}z}{m\text{/}z}\propto Q_{\mathrm{real}}& \left(24\right)\end{array}$
In FIG. 5B is shown the correlation of the relative m/z shift of the mass peaks of a mass spectrum of an ion package detected with an ion trapping mass analyser with the visible total charge Q.sub.v of the ion package derived from its detected mass spectrum.

(58) The first correlation 500 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of reference ions of a reference sample, when the real total charge Q.sub.real of the ion package is only partially visible in a detected mass spectrum as visible total charge Q.sub.v,ref. This correlation 500 is provided by a linear function, a straight line. The slope of this function, the reference slope, is a standard value, which is only related to the reference sample and to the type of the particular ion trapping mass analyser being used and defined by the geometry and the electromagnetic fields of the specific mass analyser type. In FIG. 5B is also shown optimised visible total charge Q.sub.ref,opt of the reference sample of the ion trapping mass analyser on the horizontal axis showing the visible total charge Q.sub.v. Therefore it can be deduced from the first correlation 500 the relative m/z shift of a mass spectrum, when an ion package of reference ions of the optimised visible total charge Q.sub.ref,opt of the reference ions is analysed in the ion trapping mass analyser having the optimised real total charge Q.sub.opt, which has to be also the relative m/z shift of the real optimised total charge Q.sub.opt of the ion package of reference ions. This relative m/z shift of the mass spectrum of the ion package of the optimised total charge Q.sub.opt is having the value:

(59) 0$\begin{array}{cc}{\left(\frac{\Delta m/z}{m/z}\right)}_{\mathrm{opt}}& \left(25\right)\end{array}$

(60) The second correlation 420 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of sample ions of a sample, which shall be analysed, when the real total charge Q.sub.real of the ion package of the sample ions is only partially visible in a detected mass spectrum. Also, this correlation 420 is provided by a linear function, a straight line. But the function has a greater slope compared to the reference sample, because the visible total charge Q.sub.v of the sample ions which can be derived from a mass spectrum is reduced compared to the reference sample.

(61) It should be emphasised again that the values of the relative m/z values and visible charge observed for specific measured mass spectra may deviate from this linear correlation due to measurement errors and higher-order physical effects. This has to be taken into account when the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the sample ions detected with the ion trapping mass analyser is determined as explained in detail before.

(62) For the relative m/z shift at the optimised total charge Q.sub.opt

(63) $\begin{array}{cc}{\left(\frac{\Delta m/z}{m/z}\right)}_{\mathrm{opt}}& \left(26\right)\end{array}$
can be determined the visible total charge Q.sub.v,opt. When this visible total charge Q.sub.v,opt is derived from a mass spectrum of the sample ions detected with the ion trapping mass analyser, described by the correlation 420, the investigated ion package of the sample ions is actually comprising the optimised total charge Q.sub.opt.

(64) Therefore, when the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, the optimised accumulation time t.sub.opt,real to detect the ion package of sample ions of the optimised total charge Q.sub.opt,ref can be derived from the total ion current of the visible charge TIC.sub.v shown by the second correlation 120 in FIG. 2B:

(65) $\begin{array}{cc}TI{C}_v=\frac{Q_{\mathrm{ref},\mathrm{opt}}}{t_{\mathrm{opt},v}}=\frac{Q_{v,\mathrm{opt}}}{t_{\mathrm{opt},\mathrm{real}}}& \left(27\right)\end{array}$

(66) So the optimised accumulation time t.sub.opt,real of a sample ions, whose real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, is correlated with the ion injection time period t.sub.opt,v of sample ions in the ion storage unit to perform a mass analysis of ions, which is related to the optimised visible total charge Q.sub.ref,opt of the reference sample, determined from the visible total charge Q.sub.v in the detected mass spectra of the sample ions:

(67) $\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}{t}_{\mathrm{opt},v}& \left(28\right)\end{array}$
The ratio Q.sub.v,opt/Q.sub.ref,opt can be derived from the correlations in FIG. 5B taking into account the reference slope s(reference) of the correlation 500 of an reference sample and the sample slope s(sample) of the correlation 420 of the sample, for which the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum.

(68) $\begin{array}{cc}\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}=\frac{s\left(\mathrm{reference}\right)}{s\left(\mathrm{sample}\right)}& \left(29\right)\end{array}$
The inventive method of the claims 1, 2 and 5 is now using this correlation and is determining the correlation factor c:

(69) $\begin{array}{cc}C=\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}=\frac{s\left(\mathrm{reference}\right)}{s\left(\mathrm{sample}\right)}& \left(30\right)\end{array}$
So the correlation factor c is determined by dividing the reference slope s(reference) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the reference ions detected with the ion trapping mass analyser by the sample slope s(sample) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser.

(70) Then the optimised accumulation time t.sub.opt,real of sample ions, whose total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, is correlated with the ion injection time period t.sub.opt,v of sample ions in the ion storage unit, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample and determined from the visible total charge Q.sub.v of the sample ions, as described above:
t.sub.opt,real=ct.sub.opt,v  (31)

(71) The reference slope s(reference) of the correlation 500 of the reference sample is a standard value, which is only related to the reference sample and to the type of used ion trapping mass analyser. The reference slope s(reference) is the standard ratio of the type of used ion trapping mass analyser of the relative m/z shift to the visible total charge Q.sub.v,cl of a mass spectrum of the reference ions and of the difference of the relative m/z shift to the difference of the visible total charge Q.sub.v,ref of two amounts of reference ions trapped in the ion trapping mass analyser and can be determined by a calibration process of the ion trapping transform mass analyser. These values can be determined directly from the mass spectra detected during the calibration process, when at least for one of the reference ions the m/z ratio is known. Then the reference slope is determined in the same way as the sample slope in the method of the claim 5.

(72) It can be sufficient to determine by the calibration process the reference slope of the type of used ion trapping mass analyser regarding the reference sample by executing the calibration process only for one or a few instruments. Preferably the standard value of the reference slope of the type of used ion trapping mass analyser is determined by averaging the reference slope s(reference) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the mass spectra of reference ions determined for the few instruments. As usual the reference slope s(reference) can be determined from test measurements (pre-experiments) of the reference sample defining the correlation 500. In particular the reference slope s(reference) can be determined using a linear fit, which is applied to the correlation 500 defined by the test measurements (pre-experiments).

(73) If no reference ion of the reference sample has a known m/z value, if would be also possible to determine the reference slope of the reference sample according to the approach of the method of claim 2 to determine a sample slope. Then mass spectra of different amounts of reference ions have to be detected and from these mass spectra the observable difference of a relative m/z shift has to be evaluated from the detected mass spectra of at least two of the different amounts of the reference ions by determination of the relative difference of m/z values of at least one species of reference ions from these detected mass spectra. Additional the visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v has to be evaluated from the detected mass spectra of the at least two of the different amounts of the reference ions. Then the reference slope can be determined from the evaluated observable difference of the relative m/z shift and the evaluated values of the visible total charge Q.sub.v and/or the difference of a visible total charge Q.sub.v as explained in detail before for the determination of the sample slope. The sample slope s(sample) of the correlation 420 of the sample, for which the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, can be determined by prescans of different amounts of the investigated sample ions in the ion trapping transform mass analyser.

(74) In FIG. 5B the sample slope s(sample) is determined by two pre-experiments prescan1 and prescan2, in which for two different amounts of sample ions a mass spectrum is detected in the ion trapping mass analyser. The ion injection time period of the investigated sample ions in the ion storage unit of these prescans is shown in FIG. 2B. The prescan1 is shown by the circle 160 having an ion injection time period t.sub.pre1 and the prescan2 is shown by the circle 170 having an ion injection time period t.sub.pre2. The parameters of prescan1 are shown in FIG. 5B by the circle 430 and the parameters of prescan2 are shown in FIG. 5B by the circle 440.

(75) In this embodiment the sample slope s(sample) is evaluated by the steps: Evaluation of the observable difference of a relative m/z shift from the detected mass spectra of of prescan1 and prescan2 by determination of the relative difference of m/z values of at least one species of sample ions from the mass spectra of prescan1 and prescan2 Evaluation the difference of a visible total charge Q.sub.v from the detected mass spectra of prescan1 and prescan2 of the amounts of sample ions trapped in the ion trapping mass analyser Determination of the sample slope s(sample) by calculating the ratio of the evaluated observable difference of the relative m/z shift of the mass spectra of prescan1 and prescan2 to the evaluated difference of the visible total charge of the mass spectra of prescan1 and prescan2.
This approach is used in the inventive method of claim 2 and can be used in the inventive method of claim 1 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into a ion trapping mass analyser to perform a mass analysis of sample ions, which enables a mass analysis with ion packages of sample ions of the optimised total charge Q.sub.opt, when the real total charge Q.sub.real of an ion package of the sample ions is not visible in and/or derivable from a detected mass spectrum. The method relies only on the measurements of mass spectra with the ion trapping mass analyser and the AGC approach to derive the visible total charge Q.sub.v from the detected mass spectra. Other charge detection is not required in the ion trapping mass spectrometer.

(76) The steps of the inventive method of claim 2 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into an ion trapping mass analyser to perform a mass analysis of sample ions are shown in FIG. 6. These steps can be also executed in the inventive method of claim 1.

(77) In the first step 600 mass spectra are detected by the ion trapping mass analyser for different amounts of the sample ions. The different amounts of the sample ions are injected from the ion storage unit into the ion trapping mass analyser. It may be sufficient to detect the mass spectra of two different amounts of sample ions. But also a larger number of mass spectra of different amounts of sample ions can be detected.

(78) In a following step 610 the mass spectra of the different amounts of the sample ions are compared to evaluate the observable difference of a relative m/z shift from the mass spectra.

(79) In two mass spectra, for which the observable difference shall be evaluated, For at least one species of sample ions a peak is identified which is assigned to the species of sample ions and then is determined the relative difference of the m/z values of the identified peaks, which is the relative difference of the m/z values of the species of sample ions. The relative difference of m/z values of the at least one species of the ions can be also evaluated using a large number of species of sample ions observed in the mass spectra of the different amounts of the sample ions. Therefore lists of mass peaks observed in the two mass spectra can be compared and similar peak structures can be identified e.g. by having similar peak distances (difference of their m/z ratios) and/or intensity ratios. Then the centroids of the peaks assigned to specific species of sample ions are compared to determine the relative difference of the m/z values of the specific species of sample ions in the two mass spectra. The relative difference of the m/z values can be determined regarding the m/z values of the peaks of one of the two mass spectra or regarding the average value of both m/z values.

(80) Based on the determined relative difference of the m/z values of the specific species of sample ions is the observable difference of a relative m/z shift of the two mass spectra evaluated:

(81) $\begin{array}{cc}{\delta \left(\frac{\Delta m/z}{m/z}\right)}_{ob}& \left(32\right)\end{array}$
The observable difference of the relative m/z shift of the two mass spectra is evaluated from the determined relative difference of the m/z values of the at least one species of ions by a method which is deriving from these determined relative differences of the at least one species of ions a typical relative difference of the m/z values. Accordingly the observable difference of the relative m/z shift of the two mass spectra is the determined typical relative difference of the m/z values.

(82) As already described before, the observable difference of a relative m/z shift of the two mass spectra can be preferably evaluated e.g. by averaging the determined relative difference of the m/z values of the at least one species of sample ions. Accordingly the observable difference of the relative m/z shift of the two mass spectra is in this embodiment the determined average of the determined relative difference of the m/z values of the at least one species of sample ions.

(83) Preferably the observable difference of a relative m/z shift is determined for two mass spectra as the average value of the relative difference of the m/z values of all investigated species of sample ions.

(84) To identify peaks of the same sample ion in two mass spectra for example in an embodiment of the inventive methods of the claims 1 and 2 for each of the peaks in the list of mass peaks of one mass spectrum it is searched in the list of mass peaks of the other mass spectrum, whether there is a peak where the mass (m/z values) match within a certain tolerance range (for example 20 ppm).

(85) To identify peaks of the same sample ion in two mass spectra in another embodiment of the inventive methods of the claims 1 and 2 for each of the peaks in the list of mass peaks of one mass spectrum it is searched in the list of mass peaks of the other mass spectrum, whether there is a peak where the intensity, the relative abundance value, (peak height) match within a certain tolerance range in a common mass range. Two mass peaks of the two mass spectra match, if the ratio of their intensities is not higher than 3, preferably not higher than 1.7 and preferably not higher than 1.3 (ratio of the higher to the lower intensity).

(86) To identify peaks of the same sample ion in two mass spectra in a preferred embodiment of the inventive methods of the claims 1 and 2 for each of the peaks in the list of mass peaks of one mass spectrum it is searched in the list of mass peaks of the other mass spectrum, whether there is a peak where the mass (m/z values) match within a certain tolerance range (for example 20 ppm) and the intensity (peak height) match within a certain tolerance range.

(87) The evaluation of the observable difference of a relative m/z shift from mass spectra of the different amounts of the sample ions can be executed by automated processing, which is in particular comparing the lists of mass peaks of the mass spectra.

(88) In a preferred embodiment the observable difference of a relative m/z shift is evaluated for two detected mass spectra of different amounts of sample ions.

(89) This is shown in FIG. 7, showing schematically for illustration the mass spectra of a sample ions, wherein the sample ions of the observed ion packages are injected into the ion storage unit in two different injection time periods t.sub.inj,1 and t.sub.inj,2.

(90) For the observed peaks 700 and 710 is shown the mass shift by the difference δ(Δm/z).sub.1 and δ(Δm/z).sub.2 of the m/z values of the peaks 700 and 701 which are determined as the m/z values of the peak centroids. The differences of the m/z values of the same sample ions are determined by comparing the mass spectra. From the difference δ(Δm/z).sub.1 and δ(Δm/z).sub.2 of the m/z values of the peaks 700 and 710 can deduced their relative difference, e.g. regarding their m/z value of the first mass spectrum of sample ions injected during the injection time period t.sub.inj, resulting in the relative differences of the m/z values δ(Δm/z).sub.1/(m/z.sub.1) of the peak 700 and δ(Δm/z).sub.2/(m/z.sub.2) of the peak 710 and the corresponding species of sample ions. The observable difference of the relative m/z shift of the mass spectra of the sample ions is then the average of both relative differences of the m/z values of the peaks 700 and 710.

(91) If mass spectra of more than two different amounts of sample ions have been detected, the observable difference of a relative m/z shift can evaluated for pairs of detected mass spectra of different amounts of sample ions. The observable difference of a relative m/z shift can be evaluated from different pairs of detected mass spectra by determination of the relative difference of m/z values of the same species of sample ions or different species of sample ions. It is not important to use the same species of sample ions, because the observable difference of a relative m/z shift of two mass spectra is a value which is only related to the amount of sample ions and not to specific sample ions.

(92) In another step 620, shown in FIG. 6 as the following step, the detected mass spectra of the different amounts of the sample ions are evaluated to determine the visible total charge Q.sub.v of the different amounts of the sample ions trapped in the ion trapping mass analyser or to determine the difference of the visible total charge Q.sub.v δ(Q.sub.v) of pairs of the different amounts of the sample ions trapped in the ion trapping mass analyser. Preferably the difference δ(Q.sub.v) of the visible total charge Q.sub.v of two different amounts of the sample ions is determined by subtraction of the visible total charges Q.sub.v determined for each amount of the sample ions.

(93) In a preferred embodiment, the visible total charge Q.sub.v and/or the difference δ(Q.sub.v) of the visible total charge Q.sub.v is evaluated for the detected mass spectra of two different amounts of sample ions.

(94) If mass spectra of more than two different amounts of ions have been detected, the visible total charge Q.sub.v can be in one embodiment of the invention evaluated for each detected mass spectrum or some of the detected mass spectra.

(95) If mass spectra of more than two different amounts of ions have been detected, the difference δ(Q.sub.v) of the visible total charge Q.sub.v can evaluated for pairs of two detected mass spectra of different amounts of sample ions in an embodiment of the invention.

(96) In the next step 630, the results of the two preceding steps are used to determine the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser. The sample slope provides for two amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of the difference of their relative m/z shift and their difference of the visible total charge Q.sub.v,pre of their mass spectra detected with the ion trapping transform mass analyser. The sample slope describes how the change of the relative m/z shift in the mass spectra of the sample ions is correlated with the visible total charge Q.sub.v which can be determined from a detected mass spectrum of the sample ions.

(97) In a preferred embodiment, in step 630 the results of the two preceding steps are used to calculate for two different amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of their observable difference of the relative m/z shift evaluated from their detected mass spectra to their difference of the visible total charge Q.sub.v of the sample ions trapped in the ion trapping mass analyser evaluated from their detected mass spectra. The calculated ratio corresponds to the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the mass spectra of the sample ions detected with the ion trapping mass analyser.

(98) In another embodiment, in step 630 the results of the two preceding steps are used to calculate for pairs of two different amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of their observable difference of the relative m/z shift evaluated from their detected mass spectra to their difference of the visible total charge Q.sub.v of the sample ions trapped in the ion trapping mass analyser evaluated from their detected mass spectra.

(99) Then from the calculated ratios of the pairs of different amounts of sample ions a ratio can be determined for two amounts of sample ions in general, e.g. by averaging the calculated values of the ratio. This determined ratio corresponds to the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser.

(100) In another preferred embodiment the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser is determined, preferably calculated, by a linear fit, which is taking into account the observable difference of a relative m/z shift and the visible total charge Q.sub.v and/or the difference δ(Q.sub.v) of the visible total charge Q.sub.v evaluated from pairs of two detected mass spectra of different amounts of sample ions. Based on this values and/or differences the correlation of the relative m/z shift of the mass peaks of mass spectra of ion packages of sample ions detected with the ion trapping mass analyser with the visible total charge Q.sub.v of the ion packages of sample ions derived from their detected mass spectra is provided, which can be adapted by an linear fit with a linear function. The slope of this linear function is then the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the sample ions detected with the ion trapping mass analyser.

(101) Because the correlation of the relative m/z shift of the mass peaks of mass spectra of ion packages of investigated sample ions detected with a ion trapping mass analyser with the visible total charge Q.sub.v of the ion packages derived from their detected mass spectra is a linear function, by the determined sample slope of the function the relative m/z shift can be determined for any visible total charge Q.sub.v of an amount of investigated sample ions. This correlation can be used in the inventive method of the claim 10 to correct the m/z shift observed in a mass spectrum, when the complete total charge Q.sub.real of an ion package of sample ions is not visible in and/or derivable from the detected mass spectrum of the sample ions detected with an ion trapping mass analyser, however the visible total charge Q.sub.v of the ion package of the sample ions can be derived from its detected mass spectrum.

(102) In following step 640 of the inventive method, a compensation factor c is determined. The compensation factor c is used for adjusting the ion injection time period t.sub.opt,v of sample ions, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample, into the ion storage unit to perform a mass analysis of sample ions. The optimised visible charge Q.sub.ref,opt of the reference sample is that amount of the visible total charge Q.sub.v, which is visible in a mass spectrum of the reference sample, when the real total charge Q.sub.real of investigated amount of reference ions has the value of the optimised total charge Q.sub.opt. The ion injection time period t.sub.opt,v, is defining that ion injection time period of sample ions into the ion storage unit, due to which the optimised visible charge Q.sub.ref,opt of a reference sample is observed as visible charge in a mass spectrum of the sample ions. The ion injection time period t.sub.opt,v of sample ions is determined from the visible total charge Q.sub.v evaluated from at least one mass spectrum detected with the ion trapping mass analyser of at least one amount of the sample ions and the corresponding injection time period of the sample ions. Due to the observed linear correlation of the visible total charge Q.sub.v of the at least one mass spectrum and the corresponding injection time period of sample ions the ion injection time period t.sub.opt,v of sample ions is determined. The compensation factor c is determined by dividing the reference slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of reference ions of the reference sample, which is preferably a clean sample, by the sample slope determined in step 630.

(103) In a preferred embodiment the sample slope is determined in step 630 from the detected mass spectra of two different amounts of sample ions is used in step 640 to determine the compensation factor c. The sample slope of the sample is calculated by the ratio of the observable difference of the relative m/z shift evaluated from the detected mass spectra of the two different amounts of sample ions and the difference of the visible total charge Q.sub.v evaluated from the detected mass spectra of the two different amounts of sample ions trapped in the ion trapping mass analyser.

(104) In another preferred embodiment the calculated ratio of the observable difference of the relative m/z shift to the difference of the visible total charge Q.sub.v of pairs of two different amounts of the sample ions, as described in detail in the paragraph before, can be used in step 640 as the sample slope to determine the compensation factor c for each pair of two different amounts of the sample ions. Then a general compensation factor c is determined by averaging the compensation factors c determined for each pairs of two different amounts of sample ions.

(105) This above described approach to determine the optimised accumulation time t.sub.opt,real of sample ions, whose real total charge Q.sub.real of the ion package of sample ions a sample is only partially visible in a detected mass spectrum detected with an ion trapping mass analyser, is also used in the inventive method of claim 9 to perform a mass analysis of the sample ions in the ion trapping mass analyser.

(106) A flow chart of this method is shown in FIG. 8. The method is also using the steps 600, 610, 620, 630, 640 described before regarding FIG. 6. Additionally, the optimised real injection time period t.sub.opt,real of the sample ions in the ion storage unit to perform a mass analysis of the sample ions is determined in step 800 to perform the mass analysis with an ion package of the optimised total charge Q.sub.opt. The determined compensation factor c is used to determine the real ion injection time period t.sub.opt,real, which is defined by:
t.sub.opt,real=ct.sub.opt,v  (33)

(107) Then in step 810 a mass analysis of sample ions is performed in the ion trapping mass analyser using real optimised ion injection time period t.sub.opt,real to inject sample ions into the ion storage unit of the ion trapping mass spectrometer. The mass analysis, in particular the detection of a mass spectrum, is thereby performed with an optimised amount of sample ions for a sample having the real total charge Q.sub.opt, wherein this real total charge is not visible in the detected mass spectrum.

(108) Several of the processes of the inventive methods can be supported by computers and processors, being stand alone or connected or in a cloud system and by software to execute the processes.

(109) The inventive methods might be used for each ion trapping mass spectrometer, when the m/z shift observed in mass spectra is in at least one detectable mass range of sample ions higher than 10% of the value of the accuracy of the ion trapping mass spectrometer to determine a position of a peak of ions, which is the m/z value of the peak of the ions, typically of the centroid or maximum of the peak.

(110) So the m/z shift due to different amounts of analysed sample ions cannot be observed due to a low accuracy of the position of a peak.

(111) The inventive methods might be preferably used for each ion trapping mass spectrometer, when the m/z shift observed in mass spectra is in at least one detectable mass range of sample ions higher than 50% of the value of the accuracy of the ion trapping mass spectrometer to determine a position of a peak of ions.

(112) The inventive methods might be more preferably used for each ion trapping mass spectrometer, when the m/z shift observed in mass spectra is in at least one detectable mass range of sample ions higher than 100% of the value of the accuracy of the ion trapping mass spectrometer to determine a position of a peak of ions.

(113) The inventive methods might be in particular preferably used for each ion trapping mass spectrometer, when the m/z shift observed in mass spectra is in at least one detectable mass range of sample ions higher than 200% of the value of the accuracy of the ion trapping mass spectrometer to determine a position of a peak of ions.

(114) Some investigated samples comprise at least one standard component. When for at least one sample ion generated by ionisation from a standard component comprised in the sample the m/z ratio is known, the inventive method of claim 5 can be used for determining a parameter for controlling the amount of sample ions injected from the ion storage unit into the ion trapping mass analyser to perform a mass analysis of the sample ions, which is the compensation factor c.

(115) In FIG. 2C is shown the correlation between the visible total charge Q.sub.v of the ion package stored in the ion storage unit and the injection, i.e. accumulation, time t.sub.inj of the ions, i.e. time taken to accumulate ions in the ion storage unit. The visible total charge Q.sub.v can be derived from a mass spectrum detected by the ion trapping mass analyser to which the ion package is injected from the ion storage unit as explained before. The correlation is shown for the ion packages of two different samples injected into the ion storage unit with the same total ion current TIC, which is taking into account the real total charge of the ions Q.sub.real. The correlation 180 shows the correlation when the complete total charge Q.sub.real of the ion package of reference ions of a reference sample is only partially visible as visible total charge Q.sub.v,ref in a detected mass spectrum, so that Q.sub.v,ref<Q.sub.real. Due to a constant total ion current TIC of reference ions from the ion source the correlation is provided by a linear function, a straight line. When a prescan 182 is executed as explained above with the injection time period of the prescan t.sub.pre and the visible charge Q.sub.v,pre is determined from the mass spectrum of the prescan 182, the optimised accumulation time t.sub.opt,ref of the reference ions can be determined for an optimised total charge Q.sub.ref,opt of the reference ions of the ion trapping mass analyser by the formula already described before:

(116) $\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=t_{\mathrm{opt},\mathrm{ref}}=\frac{Q_{\mathrm{ref},\mathrm{opt}}}{Q_{v,\mathrm{pre}}}{t}_{\mathrm{pre}}& \left(34\right)\end{array}$

(117) The second correlation 120 shows the correlation of the injection time period t.sub.inj and the visible total charge Q.sub.v, when the real total charge Q.sub.real of the ion package of sample ions of a sample, which shall be analysed, is not completely visible in a detected mass spectrum, so that Q.sub.v<Q.sub.real.

(118) The sample comprises at least one standard component. The m/z ratio of at least one sample ion generated by ionisation of the at least one standard component is known.

(119) Further the visible total charge Q.sub.v of the sample ions, which shall be analysed, is smaller than visible total charge Q.sub.v,ref of the reference sample, so that Q.sub.v<Q.sub.v,ref<Q.sub.real. If now the injection time period would be optimised according the formula mentioned before, the reduced amount of the visible total charge Q.sub.v would result in an increased injection time period t.sub.opt,v which is related to the optimised visible charge Q.sub.opt,ref of the reference sample, because it is determined from the visible total charge Q.sub.v evaluated from detected mass spectra of sample ions. Therefore another method is required to define an optimised accumulation time t.sub.opt,real when the visible total charge Q.sub.v,ref of an ion package of a reference sample is not completely visible in detected mass spectrum of the sample, which shall be investigated.

(120) It should be noted, that it is also possible, that the visible total charge Q.sub.v of the sample ions can be larger than the visible total charge Q.sub.v,ref of the reference ions of a reference sample.

(121) To solve the problem to determine the optimised injection time period t.sub.opt,real, when not all charges are visible in a mass spectrum, the invention uses the effect that the relative m/z shift of the mass peaks in a mass spectrum induced by the space charge of the ion package is related to the real charge Q.sub.real of an ion package, wherein the relative m/z shift of the mass peaks is proportional to the real charge Q.sub.real.

(122) $\begin{array}{cc}\frac{\Delta m/z}{m/z}\propto Q_{\mathrm{real}}& \left(35\right)\end{array}$

(123) In FIG. 5C is shown the correlation of the relative m/z shift of the mass peaks of a mass spectrum of an ion package detected with an ion trapping mass analyser with the visible total charge Q.sub.v of the ion package derived from its detected mass spectrum.

(124) The first correlation 500 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of a reference sample, when the real total charge Q.sub.real of the ion package is only partially visible in a detected mass spectrum as visible total charge Q.sub.v,ref. This correlation 500 is provided by a linear function, a straight line. The slope of this function, the reference slope, is a standard value, which is only related to the reference sample and to the type of the particular ion trapping mass analyser being used and defined by the geometry and the electromagnetic fields of the specific mass analyser type. In FIG. 5C is also shown optimised visible total charge Q.sub.ref,opt of the reference sample of the ion trapping mass analyser on the horizontal axis showing the visible total charge Q.sub.v. Therefore it can be deduced from the first correlation 500 the relative m/z shift of a mass spectrum, when an ion package of the optimised visible total charge Q.sub.ref,opt of the reference sample is analysed in the ion trapping mass analyser having the optimised real total charge Q.sub.opt, which has to be also the relative m/z shift of the real optimised total charge Q.sub.opt of the ion package of reference ions. This relative m/z shift of the mass spectrum of the ion package of the optimised total charge Q.sub.opt is having the value:

(125) $\begin{array}{cc}{\left(\frac{\Delta m/z}{m/z}\right)}_{\mathrm{opt}}& \left(36\right)\end{array}$

(126) The second correlation 460 shows the correlation of the relative m/z shift of the mass peaks with the visible total charge Q.sub.v of sample ions of a sample, which shall be analysed, when the total charge Q.sub.real of the ion package is only partially visible in a detected mass spectrum and the m/z ratio of at least one of the sample ions is known. Also, this correlation 460 is provided by a linear function, a straight line. But the function has a greater slope compared to the reference sample, because the visible total charge Q.sub.v which can be derived from a mass spectrum is reduced compared to the reference sample.

(127) It should be emphasised again that the values of the relative m/z values and visible charge observed for specific measured mass spectra may deviate from this linear correlation due to measurement errors and higher-order physical effects. This has to be taken into account when the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the sample is determined as explained in detail before.

(128) For the relative m/z shift at the optimised total charge Q.sub.opt

(129) 0$\begin{array}{cc}{\left(\frac{\Delta m/z}{m/z}\right)}_{\mathrm{opt}}& \left(37\right)\end{array}$
the visible total charge Q.sub.v,opt can be determined. When this visible total charge Q.sub.v,opt is derived from a mass spectrum of the sample ions, described by the correlation 460, the investigated ion package of the sample ions is actually comprising the optimised total charge Q.sub.opt.

(130) Therefore, when the real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum, the optimised accumulation time t.sub.opt,real to detect the ion package of the optimised total charge Q.sub.opt,ref can be derived from the total ion current of the visible charge TIC.sub.v shown by the second correlation 120 in FIG. 2C:

(131) $\begin{array}{cc}TI{C}_v=\frac{Q_{\mathrm{ref},\mathrm{opt}}}{t_{\mathrm{opt},v}}=\frac{Q_{v,\mathrm{opt}}}{t_{\mathrm{opt},\mathrm{real}}}& \left(38\right)\end{array}$
So the optimised accumulation time t.sub.opt,real of a sample ions, whose real total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum and for which the m/z ratio of at least one of the sample ions is known, is correlated with the ion injection time period t.sub.opt,v of sample ions in the ion storage unit to perform a mass analysis of ions, which is related to the optimised visible total charge Q.sub.ref,opt of the reference sample, determined from the visible total charge Q.sub.v in the detected mass spectra of the sample ions:

(132) $\begin{array}{cc}{t}_{\mathrm{opt},\mathrm{real}}=\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}{t}_{\mathrm{opt},v}& \left(39\right)\end{array}$

(133) The ratio Q.sub.v,opt/Q.sub.ref,opt can be derived from the correlations in FIG. 5C taking into account the reference slope s(reference) of the correlation 500 of an reference sample and the sample slope s(sample) of the correlation 460 of the sample, for which total charge Q.sub.real of the ion package of ions ionised from a sample is only partially visible in a detected mass spectrum and the m/z ratio of at least one of the sample ions is known.

(134) $\begin{array}{cc}\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}=\frac{s\left(\mathrm{reference}\right)}{s\left(\mathrm{sample}\right)}& \left(40\right)\end{array}$
The inventive method of the claims 1, 2 and 5 is now using this correlation and is determining the correlation factor c:

(135) $\begin{array}{cc}C=\frac{Q_{v,\mathrm{opt}}}{Q_{\mathrm{ref},\mathrm{opt}}}=\frac{s\left(\mathrm{reference}\right)}{s\left(\mathrm{sample}\right)}& \left(41\right)\end{array}$
So the correlation factor c is determined by dividing the reference slope s(reference) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the reference ions detected with the ion trapping mass analyser by the sample slope s(sample) of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser.

(136) Then the optimised accumulation time t.sub.opt,real of sample ions, whose total charge Q.sub.real of the ion package of sample ions is only partially visible in a detected mass spectrum and for which the m/z ratio of at least one of the sample ions is known, is correlated with the ion injection time period t.sub.opt,v of sample ions in the ion storage unit, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample and determined from the visible total charge Q.sub.v, as described above:
t.sub.opt,real=ct.sub.opt,v  (42)
The reference slope s(reference) of the correlation 500 of the reference sample is a standard value, which is only related to the reference sample and to the type of used ion trapping mass analyser as explained before.

(137) In FIG. 5C the sample slope s(sample) is determined by one pre-experiment named prescan-s, in which one amount of sample ions a mass spectrum is detected in the ion trapping mass analyser. The ion injection time period of the investigated sample ions in the ion storage unit of the pre-experiment prescan-s is shown in FIG. 2C. The pre-experiment prescan-s is shown by the circle 190 having an ion injection time period t.sub.pre. The parameters of pre-experiment prescan-s are shown in FIG. 5C by the circle 470.

(138) In this embodiment the sample slope s(sample) is evaluated by the steps: Evaluation of the relative m/z shift from the detected mass spectrum of the pre-experiment prescan-s by determination of the relative difference of m/z value of at least one sample ion, for which the m/z ratio is known, in the detected mass spectrum to its known m/z ratio Evaluation a visible total charge Q.sub.v from the detected mass spectrum of pre-experiment prescan-s of the amount of sample ions trapped in the ion trapping mass analyser Determination of the sample slope s(sample) by calculating the ratio of the relative m/z shift of the mass spectrum of the pre-experiment prescan-s to the evaluated visible total charge of the mass spectrum of the pre-experiment prescan-s.
This approach is used in the inventive method of claim 5 and can be used in the inventive method of claim 1 for determining a parameter for controlling the amount of sample ions injected from an ion storage unit into a ion trapping mass analyser to perform a mass analysis of sample ions, which enables a mass analysis with ion packages of sample ions of the optimised total charge Q.sub.opt, when the real total charge Q.sub.real of an ion package of the sample ions is not visible in and/or derivable from a detected mass spectrum and the m/z ratio of at least one of the sample ions is known. The method relies only on the measurements of mass spectra with the ion trapping mass analyser and the AGC approach to derive the visible total charge Q.sub.v from the detected mass spectra. Other charge detection is not required in the ion trapping mass spectrometer.

(139) The steps of the inventive method of claim 5 determining a parameter for controlling the amount of sample ions injected from an ion storage unit into an ion trapping mass analyser to perform a mass analysis of sample ions are shown in FIG. 9. These steps can be also executed of the inventive method of claim 1.

(140) In the first step 900 at least one mass spectrum is detected by the ion trapping mass analyser for at least one amount of the sample ions. The at least one amount of the sample ions is injected from the ion storage unit into the ion trapping mass analyser. It may be sufficient to detect the mass spectrum of one amount of sample ions. But also a larger number of mass spectra of different amounts of sample ions can be detected.

(141) In a following step 910 the relative m/z shift is evaluated from the at least one mass spectrum of the at least one amounts of the sample ions:

(142) $\begin{array}{cc}\left(\frac{\Delta m/z}{m/z}\right)& \left(43\right)\end{array}$
The relative m/z shift is evaluated from the at least one mass spectrum of the at least one amounts of the sample ions by determination of a relative difference of m/z value of at least one sample ion, for which the m/z ratio is known, in the at least one detected mass spectrum to its known m/z ratio.

(143) The relative difference of the m/z value in the at least one detected mass spectrum to the known m/z ratio can be determined for a large number of species of sample ions, for which the m/z ratio is known,

(144) Preferably then the relative m/z shift is determined for the least one mass spectrum of the at least one amounts of the sample ions as the average value of the determined relative differences of the m/z value of all investigated sample ions, for which the m/z ratio is known.

(145) The peak of a sample ion, for which the m/z ratio is known, can be identified in the detected mass spectrum due its specific high relative abundance, the specific peak structure of the peak pattern of sample ions, which are generated by ionisation of that specific standard component, from which the sample ion is generated by the ionisation and/or the known m/z ratio of the sample ion. More details about the identification of a peak of a sample ion, for which the m/z ratio is known, are described before.

(146) The evaluation of the relative m/z shift observed in the at least one mass spectrum of at the least one amount of the sample ions can be executed by automated processing.

(147) In another step 920, shown in FIG. 9 as the following step, the at least one mass spectrum of at least one amount of the sample ions is evaluated to determine the visible total charge Q.sub.v of at least one amount of the sample ions.

(148) In a preferred embodiment, the visible total charge Q.sub.v is evaluated from the detected mass spectra of two different amounts of sample ions.

(149) In the next step 930, the results of the two preceding steps are used to determine the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser. The sample slope provides for two amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of the difference of their relative m/z shift and their difference of the visible total charge Q.sub.v,pre of their mass spectra detected with the ion trapping transform mass analyser. The sample slope describes how the change of the relative m/z shift in the mass spectra of the sample ions is correlated with the visible total charge Q.sub.v which can be determined from a detected mass spectrum of the sample ions.

(150) In a preferred embodiment, in step 930 the results of the two preceding steps are used to calculate for one amount of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of the relative m/z shift evaluated from the detected mass spectrum of the one amount of the sample ions to the visible total charge Q.sub.v of the one amount of the sample ions trapped in the ion trapping mass analyser evaluated from the detected mass spectrum of the one amount of the sample ions. The calculated ratio corresponds to the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the mass spectra of the sample ions detected with the ion trapping mass analyser.

(151) In another embodiment, in step 930 the results of the two preceding steps are used to calculate for two different amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of their difference of the relative m/z shift evaluated from their detected mass spectra to their difference of the visible total charge Q.sub.v of the sample ions trapped in the ion trapping mass analyser evaluated from their detected mass spectra. The calculated ratio corresponds to the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of the mass spectra of the sample ions detected with the ion trapping mass analyser.

(152) In another embodiment, in step 930 the results of the two preceding steps are used to calculate for pairs of two different amounts of the sample ions injected from the ion storage unit into the ion trapping mass analyser the ratio of their difference of the relative m/z shift evaluated from their detected mass spectra and their difference of the visible total charge Q.sub.v of the sample ions trapped in the ion trapping mass analyser evaluated from their detected mass spectra.

(153) Then from the calculated ratios of the pairs of different amounts of sample ions a ratio can be determined for two amounts of sample ions in general, e.g. by averaging the calculated values of the ratio. This determined ratio corresponds to the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser.

(154) In another preferred embodiment the slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of sample ions detected with the ion trapping mass analyser is determined, preferably calculated, by a linear fit, which is taking into account the a relative m/z shift and the visible total charge Q.sub.v evaluated from the detected mass spectra of different amounts of sample ions. Based on this values the correlation of the relative m/z shift of the mass peaks of a mass spectrum of an ion package of sample ions detected with the ion trapping mass analyser with the visible total charge Q.sub.v of the ion package of sample ions derived from its detected mass spectrum is provided, which can be adapted by an linear fit with a linear function. The slope of this linear function is then the the sample slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of the sample ions detected with the ion trapping mass analyser.

(155) Because the correlation of the relative m/z shift of the mass peaks of a mass spectrum of an ion package of investigated sample ions detected with a ion trapping mass analyser with the visible total charge Q.sub.v of the ion package derived from its detected mass spectrum is a linear function, by the determined sample slope of the function the relative m/z shift can be determined for any visible total charge Q.sub.v of an amount of investigated sample ions. This correlation can be used in the inventive method of the claim 11 to correct the m/z shift observed in a mass spectrum of sample ions, when the m/z ratio of at least one of the sample ions is known and the complete total charge Q.sub.real of an ion package of sample ions is not visible in and/or derivable from the detected mass spectrum of the sample ions detected with an ion trapping mass analyser, however the visible total charge Q.sub.v of the ion package of the sample ions can be derived from the detected mass spectrum, in which the m/z shift is observed and which this m/z shift shall be corrected.

(156) In following step 940 of the inventive method, a compensation factor c is determined. The compensation factor c is used for adjusting the before explained ion injection time period t.sub.opt,v of sample ions, which is related to the optimised visible charge Q.sub.ref,opt of a reference sample, into the ion storage unit to perform a mass analysis of sample ions. The ion injection time period t.sub.opt,v of sample ions is determined from the visible total charge Q.sub.v evaluated from at least one mass spectrum detected with the ion trapping mass analyser of at least one amount of the sample ions and the corresponding injection time period of the sample ions. Due to the observed linear correlation of the visible total charge Q.sub.v of the at least one mass spectrum and the corresponding injection time period of sample ions the ion injection time period t.sub.opt,v of sample ions is determined. The compensation factor c is determined by dividing the reference slope of the linear correlation of the relative m/z shift with the visible total charge Q.sub.v of mass spectra of reference ions of the reference sample, which is preferably a clean sample, by the sample slope determined in step 930.

(157) In a preferred embodiment the sample slope is determined in step 930 from one detected mass spectrum of one amount of sample ions or detected mass spectra of two different amounts of sample ions is used in step 940 to determine the compensation factor c.

(158) If one detected mass spectrum of one amount of sample ions is used for the determination of the sample slope, the sample slope of the sample is calculated by the ratio of the relative m/z shift evaluated from one detected mass spectrum of the one amount of sample ions to the visible total charge Q.sub.v evaluated from the one detected mass spectrum of the one amount of sample ions trapped in the ion trapping mass analyser.

(159) If detected mass spectra of two different amounts of sample ions are is used for the determination of the sample slope, the sample slope of the sample san be calculated by the ratio of the difference of the relative m/z shift evaluated from the detected mass spectra of the two different amounts of sample ions and the difference of the visible total charge Q.sub.v evaluated from the detected mass spectra of the two different amounts of sample ions trapped in the ion trapping mass analyser.

(160) In another embodiment the calculated ratio of the difference of the relative m/z shift and the difference of the visible total charge Q.sub.v of pairs of two different amounts of the sample ions, as described in detail in the paragraph before, can be used in step 940 as the sample slope to determine the compensation factor c for each pair of two different amounts of the sample ions. Then a general compensation factor c is determined by averaging the compensation factors c determined for each pairs of two different amounts of sample ions.

(161) In a preferred embodiment the ratio of the relative m/z shift and the visible total charge Q.sub.v calculated for one amount of the sample ions, as described in detail before, can be used in step 940 as the sample slope to determine the compensation factor c for each of different amounts of the sample ions. Then a general compensation factor c is determined by averaging the compensation factors c determined for each of the different amounts of sample ions.

(162) The above described approach to determine the optimised accumulation time t.sub.opt,real of sample ions, whose real total charge Q.sub.real of the ion package of sample ions a sample is only partially visible in a detected mass spectrum detected with an ion trapping mass analyser, can be also used in the inventive method of claim 9 to perform a mass analysis of the sample ions in the ion trapping mass analyser, when the m/z ratio of at least one of the sample ions is known.

(163) A flow chart of this method, which is applicable when the m/z ratio of at least one of the sample ions is known, is shown in FIG. 10. The method is also using the steps 900, 910, 920, 930, 940 described before regarding FIG. 9. Additionally, the optimised real injection time period t.sub.opt,real of the sample ions in the ion storage unit to perform a mass analysis of the sample ions is determined in step 950 to perform the mass analysis with an ion package of sample ions of the optimised total charge Q.sub.opt. The determined compensation factor c is used to determine the real ion injection time period t.sub.opt,real, which is defined by:
t.sub.opt,real=ct.sub.opt,v  (44)

(164) Then in step 960 a mass analysis of sample ions is performed in the ion trapping mass analyser using real optimised ion injection time period t.sub.opt,real to inject sample ions into the ion storage unit of the ion trapping mass spectrometer. The mass analysis, in particular the detection of a mass spectrum, is thereby performed with an optimised amount of sample ions of the real total charge Q.sub.opt, wherein this real total charge of the sample ions is not visible in the detected mass spectrum and the m/z ratio of at least one of the sample ions is known.

(165) The embodiments described in this application give examples of the inventive methods, control units of an ion trapping mass spectrometer and mass spectrometers. The invention can be realised by each embodiment alone or by a combination of several or all features of the described embodiments without any limitations.