System for determining the cleanliness of mass spectrometer ion optics

1 . A mass spectrometer comprising:

an ion detector;

ion optics for guiding ions to the ion detector;

one or more voltage supply for supplying voltages to said ion optics;

control circuitry for controlling the one or more voltage supply so as to switch the ion optics between operating in a first mode in which the ion optics are unable to transmit ions having a first mass to charge ratio or first polarity to the ion detector and a second mode in which the ion optics are able to transmit ions having said first mass to charge ratio or first polarity to the ion detector for a time period; and to repeatedly switch between the first and second modes a plurality of times; and

a processor and circuitry configured to:

(i) determine the intensity of an ion signal detected by the detector at a first time in each of the time periods that the ion optics are in the second mode, and determine that these intensities vary as a function of time;

(ii) determine the intensity of the ion signal detected by the detector at a second, later time in each of the time periods that the ion optics are in the second mode, and determine that these intensities vary as a function of time; and

(iii) determine that the intensities obtained in step (i) vary with time in a different manner to the intensities obtained in step (ii) and, in response, produce a first output.

2 . The spectrometer of claim 1 , wherein the processor and circuitry are configured such that: step (i) comprises determining that the ion signal varies with time as a peak; step (ii) comprises determining that the ion signal varies with time as a peak; step (iii) comprisesdetermining that the area of the peak determined in step (i) is different from the area of the peak determined in step (ii); and step (iv) comprises producing said first output.

3 . The spectrometer of claim 2 , wherein step (iii) determines that the area of the peakdetermined in step (i) is lower than the area of the peak determined in step (ii); or

wherein step (iii) determines that the area of the peak determined in step (ii) is lower than the area of the peak determined in step (i).

4 . The spectrometer of claim 1 , wherein the processor and circuitry are configured such that: step (i) comprises determining a gradient of the ion signal at a first time in the intensity profile; step (ii) comprises determining a gradient of the ion signal at a time in the intensity profile corresponding to said first time; step (iii) comprises determining that the gradient determined in step (i) is lower than the gradient determined in step (ii); and step (iv) comprises producing said first output.

5 . The spectrometer of claim 1 , wherein processor and circuity areconfigured to:

determine how the intensities obtained in step (i) vary as a function of time;

determine how the intensities obtained in step (ii) vary as a function of time;

determine if the intensities obtained in step (i) vary with time in the same manner as the intensities obtained in step (ii); and

in response to determining that the intensities vary with time in the same manner, produce a second output.

6 . The spectrometer of claim 1 , comprising a separator for separatinganalyte molecules or ions upstream of the ion optics.

7 . The spectrometer of claim 1 , wherein the control circuitry is configuredto control the one or more voltage supply to repeatedly switch the ion optics between operating in the first and second modes a plurality of times during a single experimentalrun.

8 . A method of mass spectrometry comprising:

providing a mass spectrometer as claimed in claim 1 ; and

determining the cleanliness of the ion optics, or other condition in the spectrometer, by:

repeatedly switching the ion optics between the first mode and the second mode a plurality of times;

(i) determining the intensity of an ion signal detected by the detector at a first time in each of the time periods that the ion optics are in the second mode, and determining that these intensities vary as a function of time;

(ii) determining the intensity of the ion signal detected by the detector at a second, later time in each of the time periods that the ion optics are in the second mode, and determining that these intensities vary as a function of time; and

(iii) determining that the intensities obtained in step (i) vary with time in a different manner to the intensities obtained in step (ii) and, in response, producing a first output.

9 . A mass spectrometer comprising: an ion detector;

ion optics for guiding ions to the ion detector;

and a processor and circuitry configured to:

(i) control the ion optics so as to sequentially perform a plurality of cycles of operation during a single experimental run, wherein each cycle of operation comprises transmitting a first species of ion for a first dwell time, subsequently transmitting a second different species of ion for a second dwell time, and subsequently transmitting the first species of ion for a third dwell time;

(ii) determine the intensity of an ion signal detected by the detector during the first dwell time in each of the plurality of the cycles, and determine that these intensities vary as a function of time;

(iii) determine the intensity of an ion signal detected by the detector during the third dwell time in each of the plurality of the cycles, and determine that these intensities vary as a function of time; and

(iv) determine that the intensities obtained in step (i) vary with time in a different manner to the intensities obtained in step (ii) and, in response, produce a first output.

10 . The spectrometer of claim 9 , wherein each cycle of operation further comprises transmitting the second species of ion for a fourth dwell time, wherein the fourth dwell time is between the second and third dwell times or after the third dwell time.

11 . The spectrometer of claim 9 , wherein each cycle of operation comprises transmitting a third or further species of ion during at least one further dwell time.

12 . The spectrometer of claim 9 , comprising a separator for separating either analyte molecules in an analytical sample or separating analyte ions from an analytical sample, wherein the processor and circuitry are configured to control the ion optics so as to sequentially perform said plurality of cycles of operation during a peak that elutes from the separator.

13 . A method of mass spectrometry comprising:

providing a mass spectrometer as claimed in claim 9 ; and determining the cleanliness of the ion optics, or other condition in the spectrometer, by:

(i) performing a plurality of cycles of operation during a single experimental run, wherein each cycle of operation comprises transmitting a first species of ion for a first dwell time, subsequently transmitting a second different species of ion for a second dwell time, and subsequently transmitting the first species of ion for a third dwell time;

(ii) determining the intensity of an ion signal detected by the detector during the first dwell time in each of the plurality of the cycles, and determining that these intensities vary as a function of time;

(iii) determining the intensity of an ion signal detected by the detector during the third dwell time in each of the plurality of the cycles, and determining that these intensities vary as a function of time; and

(iv) determining that the intensities obtained in step (i) vary with time in a different manner to the intensities obtained in step (ii) and, in response, producing a first output.