Patent Publication Number: US-11640904-B2

Title: Methods for confirming charged-particle generation in an instrument, and related instruments

Description:
RELATED APPLICATIONS 
     This application is a continuation of and claims priority to U.S. application Ser. No. 16/272,621, now U.S. Pat. No. 10,903,063, filed Feb. 11, 2019, which claims the benefit of and priority to U.S. Provisional Application Ser. No. 62/629,854, filed Feb. 13, 2018, the contents of which are hereby incorporated by reference as if recited in full herein. 
    
    
     FIELD 
     The present invention relates to mass spectrometers and other instruments that generate charged particles. 
     BACKGROUND 
     Mass spectrometers are devices that ionize a sample and then determine the mass-to-charge ratios of the collection of ions formed. One well-known mass spectrometer is the Time-Of-Flight Mass Spectrometer (TOFMS), in which the mass-to-charge ratio of an ion is determined by the amount of time required for that ion to be transmitted under the influence of electric fields from the ion source to a detector. The spectral quality in the TOFMS reflects the initial conditions of the ion beam prior to acceleration into a field free drift region. Specifically, any factor that results in ions of the same mass having different kinetic energies and/or being accelerated from different points in space may result in a degradation of spectral resolution and, thereby, a loss of mass accuracy. 
     Matrix-Assisted Laser Desorption Ionization (MALDI) is a well-known method to produce gas-phase biomolecular ions for mass spectrometric analysis. The development of Delayed Extraction (DE) for MALDI-TOF has made high-resolution analysis routine for MALDI-based instruments. In DE-MALDI, a short delay is added between the ionization event, triggered by the laser, and the application of the accelerating pulse to the TOF source region. The fast (i.e., high-energy) ions will travel farther than the slow ions, thereby transforming the energy distribution upon ionization to a spatial distribution upon acceleration (in the ionization region prior to the extraction pulse application). 
     See U.S. Pat. Nos. 5,625,184, 5,627,369, 5,760,393, and 9,536,726. See also, Wiley et al.,  Time - of - flight mass spectrometer with improved resolution , Review of Scientific Instruments vol. 26, no. 12, pp. 1150-1157 (2004); M. L. Vestal,  Modern MALDI time - of - flight mass spectrometry , Journal of Mass Spectrometry, vol. 44, no. 3, pp. 303-317 (2009); Vestal et al.,  Resolution and mass accuracy in matrix - assisted laser desorption ionization - time - of - flight , Journal of the American Society for Mass Spectrometry, vol. 9, no. 9, pp. 892-911 (1998); and Vestal et al.,  High Performance MALDI - TOF mass spectrometry for proteomics , International Journal of Mass Spectrometry, vol. 268, no. 2, pp. 83-92 (2007). The contents of these documents are hereby incorporated by reference as if recited in full herein. 
     SUMMARY 
     Embodiments of the present invention are directed to methods for confirming charged-particle generation. A method to confirm charged-particle generation in an instrument may, according to some embodiments, include providing electrical connections to a charged-particle optics system of the instrument while the charged-particle optics system is in a chamber. The method may include coupling an electrical component having an impedance to charged-particle current generated in the chamber. Moreover, the method may include measuring an electrical response by the electrical component to the charged-particle current. 
     In some embodiments, providing the electrical connections to the charged-particle optics system may include grounding, or applying a voltage to, adjacent ion optics screens or plates of the charged-particle optics system. The electrical component may be a resistor that is external to the chamber, and the impedance may be a resistance value of the resistor between 10 kiloOhms (kΩ) and 100 MegaOhms (MΩ). Moreover, grounding, or applying the voltage to, adjacent ion optics screens or plates of the charged-particle optics system may include grounding an extraction plate of the charged-particle optics system, connecting a first side of the resistor to a back bias plate of the charged-particle optics system while the back bias plate is in the chamber and while the resistor is external to the chamber, connecting a power supply to a second side of the resistor while the power supply is external to the chamber, and applying the voltage via the power supply while the power supply is external to the chamber. 
     In some embodiments, the resistance value of the resistor may be between 100 kΩ and 100 MΩ. Additionally or alternatively, the method may include disconnecting a cable attached to a component of the charged-particle optics system other than the extraction plate and the back bias plate. Moreover, in some embodiments, the method may include firing a laser of the instrument toward a sample plate that is in the chamber to generate the charged-particle current in the chamber, while the extraction plate is grounded, while the first and second sides of the resistor are connected to the back bias plate and the power supply, respectively, and while the power supply is applying the voltage. Firing the laser may include firing the laser toward a sample on the sample plate, and the method may include firing the laser toward a blank slide that is free of any samples and determining whether a measurable current generated by the firing the laser toward the blank slide passes through the resistor. 
     In some embodiments, the method may include removing a downstream charged-particle optics component of the charged-particle optics system. Coupling the electrical component to the charged-particle current may be performed while the downstream charged-particle optics component is removed. 
     In some embodiments, the instrument may include a mass spectrometer, and the method may include determining that no signal is being generated by the mass spectrometer. Moreover, providing the electrical connections to the charged-particle optics system may include providing a first state of the electrical connections that is different from a previous second state of the electrical connections, in response to the determining that no signal is being generated by the mass spectrometer. 
     In some embodiments, the charged-particle current may be a measured ion current, and the method may include determining a quantity of ions that are generated in the chamber by comparing the measured ion current with a predetermined value. Moreover, the charged-particle current may be a current of an electron beam that is generated in the chamber. 
     In some embodiments, coupling may include firing a laser of the instrument toward a target that is in the chamber to generate the charged-particle current. The method may include adjusting laser energy and/or laser focus of the laser in response to the measuring the electrical response by the electrical component to the charged-particle current. Additionally or alternatively, providing the electrical connections may be performed while the chamber is under vacuum pressure. 
     A method to confirm ionization in an instrument may, according to some embodiments, include grounding a first plate or screen of an ion optics system of the instrument while the first plate or screen is in a chamber that is under vacuum pressure. The method may include connecting a first side of an electrical component having an impedance to a second plate or screen of the ion optics system while the second plate or screen is in the chamber. The method may include connecting a power supply to a second side of the electrical component while the power supply is external to the chamber. The method may include applying a voltage via the power supply while the power supply is external to the chamber. The method may include firing a laser of the instrument toward a sample plate of the instrument, while the first plate or screen is grounded, while the first and second sides of the electrical component are connected to the second plate or screen and the power supply, respectively, and while the power supply is applying the voltage. Moreover, the method may include coupling the electrical component to ion current generated from a sample that is on the sample plate while the sample plate is in the chamber. 
     In some embodiments, the instrument may include a mass spectrometer, the electrical component may be a resistor that is external to the chamber, the impedance may be a resistance value of the resistor between 100 kiloOhms (kΩ) and 100 MegaOhms (MΩ), and the method may include determining that no signal is being generated by the mass spectrometer. Moreover, the first plate or screen may be an extraction plate, the second plate or screen may be a back bias plate, and the grounding and the connecting the first side may be performed in response to the determining that no signal is being generated by the mass spectrometer. 
     In some embodiments, the method may include measuring a first electrical response by the electrical component to the ion current. The method may include firing the laser toward a blank slide that is free of any sample. Moreover, the method may include measuring a second electrical response, or detecting an absence thereof, by the electrical component to the firing the laser toward the blank slide. Additionally or alternatively, the method may include determining a quantity of ions that are generated by comparing the ion current with a predetermined value. 
     An instrument, according to some embodiments, may include a chamber that includes an ion optics system including a first plate or screen and a second plate or screen. The chamber may also include a sample plate. The instrument may include a power supply that is external to the chamber and an electrical component that is connectable between the second plate or screen and the power supply. The electrical component may have an impedance and may be configured to receive charged-particle current generated in the chamber. 
     In some embodiments, the instrument may include a mass spectrometer, the electrical component may be a resistor that is external to the chamber, and the impedance may be a resistance value of the resistor between 10 kiloOhms (kΩ) and 100 MegaOhms (MΩ). Additionally or alternatively, a deflector portion of the ion optics system may be removable from the ion optics system. 
     In some embodiments, the instrument may include a laser configured to fire toward the sample plate, while first and second sides of the resistor are connected to the second plate or screen and the power supply, respectively, and while the power supply is applying a voltage. The resistor may be configured to receive ion current generated from a sample that is on the sample plate. The resistance value of the resistor may be a predetermined value between 100 kΩ and 100 MΩ. Moreover, the first plate or screen may be an extraction plate and the second plate or screen may be a back bias plate. 
     In some embodiments, the instrument may include a shorting plug by which the extraction plate is connectable to ground. The laser may be configured to fire toward the sample plate while the extraction plate is grounded. Additionally or alternatively, the instrument may include a switch by which the extraction plate is switchably connectable to ground. The switch may be external to the chamber, and the laser may be configured to fire toward the sample plate while the extraction plate is grounded. Moreover, the instrument may include a switch, which is external to the chamber, and by which the resistor is switchably connectable between the back bias plate and the power supply. 
     Further features, advantages, and details of the present invention will be appreciated by those of ordinary skill in the art from a reading of the figures and the detailed description of the example embodiments that follow, such description being merely illustrative of the present invention. 
     It is noted that aspects of the invention described with respect to one embodiment may be incorporated in a different embodiment although not specifically described relative thereto. That is, all embodiments and/or features of any embodiment can be combined in any way and/or combination. Applicant reserves the right to change any originally-filed claim or file any new claim accordingly, including the right to be able to amend any originally-filed claim to depend from and/or incorporate any feature of any other claim although not originally claimed in that manner. These and other objects and/or aspects of the present invention are explained in detail in the specification set forth below. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG.  1 A  is a perspective view of an instrument, according to embodiments of the present invention. 
         FIG.  1 B  is a perspective view of an instrument and a light source, according to embodiments of the present invention. 
         FIG.  2 A  illustrates a schematic diagram of an instrument and a light source, according to embodiments of the present invention. 
         FIG.  2 B  illustrates a block diagram of the chamber of  FIG.  2 A , according to embodiments of the present invention. 
         FIG.  2 C  illustrates a block diagram of a processor control system of the instrument of  FIG.  2 A , according to embodiments of the present invention. 
         FIG.  2 D  illustrates a block diagram of an example processor and memory that may be used in accordance with embodiments of the present invention. 
         FIGS.  3 A- 3 E  illustrate schematic diagrams of an external resistor coupled to an ion optics system of the chamber of  FIGS.  2 A and  2 B , according to embodiments of the present invention. 
         FIGS.  4 A- 4 E  illustrate flowcharts of example methods to confirm ionization or other charged-particle generation in an instrument, according to embodiments of the present invention. 
         FIG.  5 A  illustrates a graph of oscilloscope traces for an instrument firing on a blank slide, according to embodiments of the present invention. 
         FIG.  5 B  illustrates a graph of oscilloscope traces for an instrument firing on a sample slide, according to embodiments of the present invention. 
         FIG.  6    illustrates a partial section perspective view inside the chamber of  FIGS.  2 A and  2 B , according to embodiments of the present invention. 
         FIG.  7    illustrates a block diagram of a resistor connected to a processor and a laser source for the calibration of laser energy and/or laser focusing, according to embodiments of the present invention. 
         FIG.  8    illustrates a flowchart of example methods for the calibration of laser energy and/or laser focusing, according to embodiments of the present invention. 
         FIG.  9 A  illustrates Safe High Voltage (SHV) feedthroughs that can be used with an instrument, according to embodiments of the present invention. 
         FIG.  9 B  illustrates an SHV patch cable that can be used with an instrument, according to embodiments of the present invention. 
     
    
    
     DETAILED DESCRIPTION 
     The present invention now will be described more fully hereinafter with reference to the accompanying drawings, in which illustrative embodiments of the invention are shown. Like numbers refer to like elements and different embodiments of like elements can be designated using a different number of superscript indicator apostrophes (e.g.,  10 ,  10 ′,  10 ″,  10 ″′). 
     During assembly of a mass spectrometry instrument/system, it may be advantageous to have a diagnostic to confirm the occurrence of ionization due to, for example, a MALDI process. According to embodiments of the present invention, such a diagnostic may be provided by using the existing ion optics of the instrument/system as a charge collection plate. Moreover, an external Direct Current (DC) power supply may be used to bias one of the plates of the ion optics. 
       FIG.  1 A  and  FIG.  1 B  illustrate an example instrument  10 , such as a mass spectrometer  10 M. As shown in  FIG.  1 A , the instrument  10  includes a housing  10   h  with a front wall  10   f  having a display  10   d  with a user interface. The housing  10   h  also has at least one sample specimen entry port  10   p  that can be sized and configured to receive slides. One or more ports  10   p  may be used. Each port  10   p  can be configured as entry-only, exit-only, or as both an entry-and exit-port for specimen slides (e.g., for a sample plate  230  of  FIG.  2 A ) for analysis. 
     As shown in  FIG.  1 B , an instrument  10  may use at least one light source  20 , according to embodiments of the present invention. In some embodiments, the instrument  10  may be a mass spectrometer  10 M, and the housing  10   h  may include at least one sample specimen entry port  10   p  configured to receive slides for the mass spectrometer  10 M. For example, the mass spectrometer  10 M may be a table top mass spectrometer, as shown by the table  30 . Moreover, one or more portions of the instrument  10  may be pumped/evacuated via a vacuum pump  60  to a desired pressure. The vacuum pump  60  and/or the light source  20  may be on board (e.g., inside) the housing  10   h  or may be provided as an external plug-in component to the instrument  10 . 
     The at least one light source  20  can provide light to generate ions inside the instrument  10 . For example, the light source  20  may comprise a laser  20 LS that supplies laser light to the instrument  10 . As an example, the laser  20 LS may be a solid state laser, such as an UltraViolet (UV) laser with a wavelength above 320 nanometers (nm). In some embodiments, the solid state laser  20 LS can generate a laser beam with a wavelength between about 347 nm and about 360 nm. The solid state laser  20 LS can alternatively be an infrared laser or a visible light laser. 
     Moreover, although the terms “light source” and “laser” are used to discuss examples herein, the light source  20  may comprise any type of source that generates charged particles inside the instrument  10  by supplying light/energy to a target/device inside the instrument  10 . For example, the light source  20  may be configured to provide one of various types of pulses of light/energy to a sample plate  230  ( FIG.  2 A ) in the instrument  10  to generate a pulse of charged particles. In some embodiments, the light source  20  and the sample plate  230  may collectively (or even individually) be referred to as an “ion source,” as light from the light source  20  may be directed to the sample plate  230  to generate ions. 
       FIG.  2 A  illustrates a schematic diagram of an instrument  10  and a light source  20 . The instrument  10  includes a chamber  210 , which may be an “acquisition chamber,” a “process chamber,” a “vacuum chamber,” a “chamber under vacuum,” or a “chamber in vacuum.” Inside the chamber  210  are a sample plate  230  (or other target  230 T) and an ion optics system  220 , which may also be referred to herein as “ion optics” or an “ion optics assembly.” 
     The ion optics system  220  may be configured to receive light/energy  20 L from the light source  20 , and to direct the light/energy  20 L to the sample plate  230 . The light/energy  20 L can cause the sample plate  230  to generate an ion current  230 C, which passes through the ion optics system  220 , through a flight tube  240 , and onto a detector  250 . The ion current  230 C may be measured as part of a diagnostic method/mode to confirm ionization in the instrument  10 . Accordingly, as used herein, the term “diagnostic” refers to a diagnostic with respect to the instrument  10  rather than with respect to a patient. 
     In addition to the ion current  230 C, the instrument  10  may, in some embodiments, provide photons  260 P from a photon source  260  onto the detector  250 . As illustrated in  FIG.  2 A , the sample plate  230  may be adjacent a first end  210 E of the acquisition chamber  210 . The first end  210 E of the acquisition chamber  210  and a second end  250 E of the detector  250  may be on opposite ends/portions of the instrument  10 . 
       FIG.  2 B  illustrates a block diagram of the chamber  210  of  FIG.  2 A . The ion optics system  220  inside the chamber  210  may include an extraction plate  221  and a back bias plate  222 . Moreover, the ion optics system  220  may include a deflector plate  223 . In some embodiments, the deflector plate  223  may be omitted or removable from the ion optics system  220 . 
     External to the chamber  210  are a resistor  201  and a power supply  202 . The resistor  201  is connectable between (e.g., switchably coupled to) the back bias plate  222  and the power supply  202 . As an example, first and second sides/ends of the resistor  201  may be connected to the back bias plate  222  and the power supply  202 , respectively. A resistance value of the resistor  201  may be between 10 kiloOhms (kΩ) and 100 MegaOhms (MΩ), such that the resistor  201  is configured to receive ion current  230 C generated from a sample on the sample plate  230 . Accordingly, the measured current that is described herein is the ion current  230 C that passes through the resistor  201 . For example, the ion current  230 C may be measured by measuring a voltage response across the resistor  201  when the ion current  230 C passes through the resistor  201 , as ion generation inside the chamber  210  results in a change in voltage and current across the resistor  201 . Moreover, the power supply  202  may be connectable between the sample plate  230  and the resistor  201 . 
     Although some examples herein describe a sample on a sample plate  230 , the light  20 L could, in some embodiments, be directed to a test plate or other target  230 T instead of the sample plate  230 . Additionally or alternatively, the combination/coupling of the resistor  201 , the power supply  202 , and the ion optics system  220  may, in some embodiments, be referred to as a “system,” such as a diagnostic system. Moreover, as the resistor  201  is outside of the vacuum chamber  210 , the resistor  201  is typically at atmospheric pressure. In some embodiments, however, the resistor  201  may be inside the vacuum chamber  210 . Additionally or alternatively, any electrical component (e.g., an inductor or a capacitor) having an impedance can be used in place of the resistor  201 , as the resistor  201  is merely one example of an electrical component having an impedance. 
       FIG.  2 C  illustrates a block diagram of a processor control system  270 C. The processor control system  270 C may include one or more processors  270 , which may be configured to communicate with the light source  20 , the resistor  201 , the detector  250 , and/or the photon source  260 . For example, operations of the light source  20  and/or the photon source  260  may be performed under the control of the processor(s)  270 . Also, a signal from the resistor  201  (e.g., a signal provided via probes coupled to the resistor  201 ) may be processed by the processor(s)  270  to measure the ion current  230 C that passes through the resistor  201 . Moreover, data generated by the detector  250  in response to receiving ions and/or photons  260 C may be provided to the processor(s)  270  for processing. The processor(s)  270  may be internal and/or external to the instrument  10 . 
       FIG.  2 D  illustrates a block diagram of an example processor  270  and memory  280  that may be used in accordance with various embodiments of the invention. The processor  270  communicates with the memory  280  via an address/data bus  290 . The processor  270  may be, for example, a commercially available or custom microprocessor. Moreover, the processor  270  may include multiple processors. The memory  280  is representative of the overall hierarchy of memory devices containing the software and data used to implement various functions as described herein. The memory  280  may include, but is not limited to, the following types of devices: cache, ROM, PROM, EPROM, EEPROM, flash, Static RAM (SRAM), and Dynamic RAM (DRAM). 
     As shown in  FIG.  2 D , the memory  280  may hold various categories of software and data, such as an operating system  283 . The operating system  283  can control operations of the instrument  10 . In particular, the operating system  283  may manage the resources of the instrument  10  and may coordinate execution of various programs by the processor  270 . 
       FIGS.  3 A- 3 E  illustrate schematic diagrams of the resistor  201  coupled to the ion optics system  220  of  FIGS.  2 A and  2 B . Referring to  FIG.  3 A , a first side of the resistor  201  is connected to the back bias plate  222  of the ion optics system  220  and a second side of the resistor  201  is connected to the power supply  202 . As discussed with respect to  FIG.  2 B , the back bias plate  222  is inside the chamber  210 , whereas the resistor  201  and the power supply  202  are external to the chamber  210 . The sample plate  230 , which is also inside the chamber  210 , generates ions  230 I that flow toward the back bias plate  222 . This flow of the ions  230 I may be referred to herein as the ion current  230 C. 
     The extraction plate  221  of the ion optics system  220  may be connected to ground (i.e., ground potential) GND. In particular,  FIG.  3 A  illustrates ion behavior when the extraction plate  221  is connected to ground GND. A reversal in electric field direction may cause ion deceleration to a velocity near zero rather than providing a velocity in an opposite/reverse direction. If the extraction plate  221  is instead connected to power, then it can provide ion travel to the back bias plate  222 , which may also be referred to herein as a “charge collection plate.” 
     The sample plate  230  may be simultaneously connected to ground GND and to the power supply  202 , which may be configured to supply a voltage under about 1000 Volts (V). For example, the power supply  202  may be configured to supply a voltage of about 200 V. Any voltage between about 30 V and about 1000 V, however, may be supplied. The sample plate  230  may be at a single voltage at a given time due to a conductive coating on the surface of the sample plate  230 . The significance of the ground GND (0 V) is to reference the voltage with respect to the other end of voltage source  202 . 
     Referring to  FIG.  3 B , the resistor  201  may serve as a Current-Viewing Resistor (CVR). Based on Ohm&#39;s law, the voltage  201 V across the resistor  201  is dependent on the magnitude of the current. As only a small current is generated during a single ionization event, the resistance value of the resistor  201  should be large enough to facilitate measuring the voltage  201 V response. The resistance value, however, should be small enough that the measured voltage  201 V will not damage test equipment, including the power supply  202  that is used to bias the back bias plate  222 . As such, resistance values between about 10 kΩ and about 100 MΩ would be appropriate for the resistor  201 . For example, the resistor  201  may have a resistance value of about 1 MΩ. In some embodiments, the resistance value may be between about 100 kΩ and about 100 MΩ. Moreover, even lower resistance values than 100 kΩ may be used given sufficient signal filtering, processing, and amplification of the measured CVR voltage  201 V. Accordingly, a resistance value as low as about 10 kΩ may be used in some embodiments. The resistance value may be a known/predetermined value. 
       FIG.  3 B  also illustrates probes  310  that can be used to measure the CVR voltage  201 V across the resistor  201 . Each probe  310  may have a resistance and a capacitance. For example, each probe  310  may have a 10 MΩ resistance and an 11 picofarad (pF) capacitance. 
     Furthermore, the ion current  230 C provided from the sample plate  230  to the back bias plate  222  may be a time-dependent ion beam current  230 C′. Also,  FIG.  3 B  shows that the pressure state  210 S of the chamber  210  may be in vacuum when the time-dependent ion beam current  230 C′ is generated and the CVR voltage  201 V is measured. It may be advantageous to perform the current/voltage measurement(s) described herein without venting the chamber  210 , as venting the chamber  210  may result in multiple hours of pumping time to return to vacuum pressures after venting. A further (and potentially more important) reason for operating in vacuum is that the ions  230 I may not reach the charge collection plate due to the decreased mean free path of the ions  230 I at higher pressures. Moreover, in some embodiments, the current/voltage measurement(s) can be performed using plates or other hardware separate from the ion optics system  220 . Although the current/voltage measurement(s) may be used for instrument diagnostics, the current/voltage measurement(s) may additionally or alternatively be used for calibration purposes, such as for laser energy adjustment or focus. 
     Referring to  FIG.  3 C , example electrical connections external to the chamber  210  are illustrated. Because the connections are external to the chamber  210 , it is possible to provide the diagnostic mode(s)/method(s) described herein for the instrument  10  without significant hardware additions. For example, switches  221 S and  222 S are shown outside of the chamber  210 . The switches  221 S and  222 S may be relays or other switches, and may be used to connect plates inside the chamber  210  to power supplies or to ground GND outside of the chamber  210 . As an example,  FIG.  3 C  illustrates that the switch  221 S selects whether (e.g., selectively connects) the extraction plate  221  is connected to ground GND or to a pulsed power supply  330 , which may be a 3-5 kiloVolt (kV) pulsed power supply. Moreover, the switch  222 S selects whether the back bias plate  222  is connected to the resistor  201  or to a third power supply  320 , which may be a 30-100 V power supply. Accordingly, the extraction plate  221  and the back bias plate  222  inside the chamber  210  may be referred to herein as being “switchably connectable” to power supplies or to ground GND outside of the chamber  210  via the switches  221 S and  222 S, respectively. 
       FIG.  3 C  further illustrates a switch  201 S that selects whether to connect the resistor  201  to the power supply  202 . When disconnected from the resistor  201 , the power supply  202  may instead be connected to the detector  250 . For example, when the instrument  10  is operating in a standard mode (e.g., a sample analysis mode) rather than a diagnostic mode, the switches  201 S and  222 S may disconnect respective ends of the resistor  201  from the power supply  202  and the back bias plate  222 . Accordingly, the resistor  201  may be referred to herein as being “switchably connectable” between the back bias plate  222  and the power supply  202  by the switch  222 S and/or the switch  201 S. 
     The CVR voltage  201 V may be measured when the switch  201 S and/or the switch  222 S connect(s) the resistor  201  between the back bias plate  222  and the power supply  202 . For example, the CVR voltage  201 V may be measured via an external oscilloscope (e.g., using the probes  310  of  FIG.  3 B ) or may be diverted to an internal digitizer within the instrument  10  (e.g., a digitizer within a mass spectrometer  10 M). Moreover, operations of the switches  201 S,  221 S, and  222 S may be controlled by the one or more processors  270  of  FIGS.  2 C and  2 D . 
     Referring to  FIG.  3 D , the extraction plate  221  may be connected to a power supply  340  instead of being connected to ground GND as shown in  FIGS.  3 A and  3 B . The power supply  340  is configured to apply a voltage to the extraction plate  221  to transmit ions  221 I from the extraction plate  221  to the back bias plate  222 . The ions  221 I may be ones of ions  230 I that arrived at the extraction plate  221  by passing from the sample plate  230  through an aperture in the back bias plate  222 . Accordingly, the voltage applied by the power supply  340  may return the ions  221 I to the back bias plate  222 . In some embodiments, the voltage supplied by the power supply  340  may be equal in magnitude and opposite in polarity to the voltage supplied by the power supply  202  to the back bias plate  222 . This may allow for a small increase in current that is collected on the back bias plate  222 , thus making the voltage response across the resistor  201  easier to detect. 
     For example, as discussed herein with respect to  FIG.  3 C , the CVR voltage  201 V across the resistor  201  may be measured via an external oscilloscope or may be diverted to an internal digitizer within the instrument  10 . The power supply  340  and the resistor  201  are external to the chamber  210  that includes the extraction plate  221 . Accordingly, the measurement of the CVR voltage  201 V while the power supply  340  is applying a voltage to the extraction plate  221  may, in some embodiments, be performed via hardware external to the chamber  210  with switchable and/or manual/releasable connections to the inside of the chamber  210 . 
     Referring to  FIG.  3 E , a power supply  350  may be connected to the extraction plate  221  to transmit the ions  221 I of  FIG.  3 D  to the back bias plate  222 . In some embodiments, the power supply  350  may supply voltages ranging from about 30 V to about 500 V. Moreover, in some embodiments, the extraction plate  221  and the back bias plate  222  may be switchably connectable to the power supply  350 . For example, the switches  221 S and  222 S may select whether to connect the extraction plate  221  and the back bias plate  222 , respectively, to the power supply  350 . When the instrument  10  is analyzing a sample, the extraction plate  221  may be connected to the pulsed power supply  330 , and the back bias plate  222  may be connected to the power supply  350 . On the other hand, when the instrument  10  is performing a diagnostic method, the extraction plate  221  may be connected to the power supply  350 , and the back bias plate  222  may be connected to the resistor  201 . 
     In some embodiments, the measured ion current  230 C may be compared with a predetermined threshold ion current value. For example, if the instrument  10  has a predetermined threshold ion current value that is suitable for mass spectra generation, the response of the diagnostic method(s) described herein may be used to confirm/set ionization. As an example, for MALDI ionization, the laser pulse energy may be fixed and the laser spot size varied, or vice versa, until the predetermined threshold ion current value is detected via the resistor  201 . 
     The method(s) described herein may be used for mass spectrometers. Any system/instrument using charged-particle optics for the acceleration of ion beams or electron beams, however, may use the method(s). Such systems/instruments may include electron microscopes, plasma thrusters, X-ray generators, ion beams for medical treatment, and ion implanters for semiconductor manufacturing, among others. Accordingly, the term “charged-particle optics system,” as used herein, is not limited to an optics system for ions. Similarly, the instrument  10  described herein may measure “charged-particle current,” which is not limited to measuring ion current. Also, the measurement(s) may be performed to confirm “charged-particle generation,” which is not limited to confirming ionization. Moreover, for electron-beam applications, the polarities of the voltages described herein with respect to ion applications would be reversed. 
       FIGS.  4 A- 4 E  illustrate flowcharts of methods to confirm ionization, or other charged-particle generation, in the instrument  10 . In some embodiments, the memory  280  of  FIG.  2 D  may be a non-transitory computer readable storage medium including computer readable program code therein that when executed by the processor  270  causes the processor  270  to perform the method(s) of any of  FIGS.  4 A- 4 E . 
     Referring to  FIG.  4 A , the methods may include providing/reconfiguring (Block  411 ) the ion optics system  220  so that the ion current  230 C inside the chamber  210  of the instrument  10  can be measured (e.g., measured via the resistor  201  external to the vacuum chamber  210 ). The method shown in  FIG.  4 A  may then include determining (Block  412 ) whether the ion current  230 C is measurable. Accordingly, ionization in the instrument  10  may be confirmed based on the operations of Blocks  411  and  412 . 
     Moreover, if the ion current  230 C is measurable (Block  412 ), then the method may include determining (Block  420 ) whether the ions  230 I are arriving at the detector  250 . On the other hand, if the ion current  230 C is not measurable (Block  412 ), then troubleshooting (Block  413 ) of ionization mechanism(s) should be performed. 
     If the ions  230 I are arriving at the detector  250  (Block  420 ), then the method may include determining (Block  430 ) whether the detector  250  is operating properly. On the other hand, if the ions  230 I are not arriving at the detector  250  or if their arrival is uncertain (Block  420 ), then the ion optics system  220  may be provided/reconfigured (Block  421 ) to iteratively measure the ion current  230 C at points along a path of the ions  230 I. 
     The method may then including determining (Block  422 ) whether it detects a measurable ion current  230 C that should arrive at the detector  250 . If so, then the method may include determining (Block  430 ) whether the detector  250  is operating properly. On the other hand, if the method does not detect a measurable ion current  230 C that should arrive at the detector  250  (Block  422 ), then troubleshooting (Block  423 ) of voltages, mechanical assemblies, and/or installation of the ion optics system  220  should be performed. 
     If the detector  250  is operating properly (Block  430 ), then it may be determined (Block  440 ) that the path of the ions  230 I is suitable. Moreover, in some embodiments, troubleshooting of other areas of the system/instrument  10  may be performed, including electronics troubleshooting and/or vacuum troubleshooting. If, on the other hand, the detector  250  is not working properly or the propriety of operation is uncertain (Block  430 ), then the method may include turning on (Block  433 ) a UV Light Emitting Diode (LED) in a pulsed operation. Before turning on (Block  433 ) the UV LED, the method may include determining (Block  431 ) whether the UV LED is installed. If not, then the UV LED may be installed (Block  432 ). In some embodiments, the UV LED may be the photon source  260  of  FIG.  2 A . 
     After turning on (Block  433 ) the UV LED, the method may include determining (Block  434 ) whether the detector  250  signal pulses during pulsing of the UV LED. If so, then the method may include determining (Block  436 ) whether the signal gain of the detector  250  is as expected, such as by comparing the signal gain with a threshold signal gain value. On the other hand, if the detector  250  does not signal pulse (Block  434 ) during pulsing of the UV LED, then troubleshooting (Block  435 ) of the detector  250  may be performed. 
     If the signal gain of the detector  250  is not as expected (Block  436 ), such as by being below a threshold signal gain value, then the method may include adjusting (Block  437 ) the gain of the detector  250 . For example, the method may include varying the output power of the UV LED (e.g., by varying the diode current) and then adjust the gain of the detector  250  based on the measured response. If, on the other hand, the signal gain of the detector  250  is as expected (Block  436 ), then operations may proceed to Block  440 , which is described above herein. 
     Referring again to Block  411 , the providing/reconfiguring of the ion optics system  220  may be performed in response to determining (Block  410 ) that the ions  230 I are not being generated, or that their generation is uncertain. If, on the other hand, it is determined that the ions  230 I are being generated (Block  410 ), then the method may proceed directly to determining (Block  420 ) whether the ions  230 I are arriving at the detector  250 , and the operations of Blocks  411  and  412  may be omitted. Moreover, in some embodiments, the instrument  10  may be a mass spectrometer  10 M, and the operation(s) of Blocks  410 ,  411 , and/or  412  may be performed in response to determining (Block  405 ) that no signal is being generated by the mass spectrometer  10 M. 
     Referring to  FIG.  4 B , the method(s) described herein are not limited to ionization. For example, the operations of Blocks  411  and  412  of  FIG.  4 A  may be performed with respect to various types of charged particles, as indicated by Blocks  411 ′ and  412 ′ of  FIG.  4 B , respectively. In particular,  FIG.  4 B  illustrates a method that includes providing/reconfiguring (Block  411 ′) electrical connections to a charged-particle optics system  220  of the instrument  10  while the charged-particle optics system  220  is in a vacuum chamber  210  that is in/under vacuum pressure. In some embodiments, the providing/reconfiguring operation(s) of Block  411 ′ may be performed automatically by the method via one or more of the switches  201 S,  221 S, and  222 S. Additionally or alternatively, one or more electrical connections may be manually provided/reconfigured, such as by manually connecting a shorting cable/plug by which the extraction plate  221  is connectable to ground GND and/or by manually disconnecting one or more cables/plugs. 
     After the providing/reconfiguring operation(s) of Block  411 ′, the method may confirm charged-particle generation in the instrument  10  by coupling (Block  412 ′) the resistor  201  that is external to the vacuum chamber  210  to charged-particle current  230 C generated in the vacuum chamber  210 . The operation(s) of Block  412 ′ may also include measuring an electrical response by the resistor  201  to the charged-particle current  230 C. In particular, the charged-particle current  230 C passing through the resistor  201  provides the voltage  201 V response that can be measured. A value of the charged-particle current  230 C may then be determined using Ohm&#39;s law. Moreover, as described herein with respect to  FIG.  2 B , a resistance value of the resistor  201  may be between 10 kΩ and 100 MΩ. 
     The operations of  FIG.  4 B  are not limited to being performed while the chamber  210  is in/under vacuum pressure. Rather, in some embodiments, a method may include venting the system, making the electrical connections at atmospheric pressure, and then testing/measuring after the system pumps down. 
     Referring to  FIG.  4 C , the providing/reconfiguring operation(s) of Block  411 ′ of  FIG.  4 B  may include multiple operations. For example, the providing/reconfiguring (Block  411 ′) of the electrical connections to the charged-particle optics system  220  may include grounding, or applying a voltage to, adjacent ion optics screens or plates of the charged-particle optics system  220 . As an example, the providing/reconfiguring operations may include grounding (Block  411 ′- 2 ) the extraction plate  221  of the charged-particle optics system  220  while the extraction plate  221  is in the vacuum chamber  210 . The providing/reconfiguring operations may also include connecting (Block  411 ′- 3 ) a first side of the resistor  201  to the back bias plate  222  of the charged-particle optics system  220  while the back bias plate  222  is in the vacuum chamber  210  and while the resistor  201  is external to the vacuum chamber  210 . Moreover, the providing/reconfiguring operations may include connecting (Block  411 ′- 4 ) the power supply  202  to a second side of the resistor while the power supply  202  is external to the vacuum chamber  210 . 
     After the operations of Block  411 ′- 2 , Block  411 ′- 3 , and Block  411 ′- 4 , which can be performed in any order, the method may include applying (Block  411 ′- 5 ) a voltage via the power supply  202  while the power supply  202  is external to the vacuum chamber  210 . Before the method applies (Block  411 ′- 5 ) the voltage, the providing/reconfiguring operations of Block  411 ′ may include disconnecting (Block  411 ′- 1 ) a cable attached to a component of the charged-particle optics system  220  other than the extraction plate  221  and the back bias plate  222 . The disconnecting of Block  411 ′- 1  may, in some embodiments, be performed before placing the chamber  210  in/under vacuum pressure. Additionally or alternatively, the component (e.g., one or more downstream charged-particle optics components) may be removed from the charged-particle optics system  220 . For example, a deflector portion/component (e.g., the deflector plate  223 ) of the charged-particle optics system  220  may be removed, and the charged-particle current  230 C may be measured while the deflector portion  223  is absent. 
     In some embodiments, the providing/reconfiguring operation(s) of Block  411 ′ may include providing a first state of electrical connections to the charged-particle optics system  220 , such as by performing one or more of the operations of Block  411 ′- 1 , Block  411 ′- 2 , Block  411 ′- 3 , and Block  411 ′- 4 . Moreover, the state of electrical connections to the charged-particle optics system  220  before the providing/reconfiguring operation(s) of Block  411 ′ may be a different second state, such as a state that precedes/lacks one or more of the operations of Block  411 ′- 1 , Block  411 ′- 2 , Block  411 ′- 3 , and Block  411 ′- 4 . 
     Referring to  FIG.  4 D , the operation(s) of Block  412 ′ of  FIG.  4 B  may include multiple operations. For example, the operations may include firing (Block  412 ′- 3 ) the laser  20  of the instrument  10  toward the sample plate  230  that is in the vacuum chamber  210 , while the extraction plate  221  is grounded, while first and second sides of the resistor  201  are connected to the back bias plate  222  and the power supply  202 , respectively, and while the power supply  202  is applying a voltage. In particular, the laser  20  may fire toward a sample that is on the sample plate  230 . The method may then include measuring (Block  412 ′- 4 ), via the resistor  201 , the current  230 C generated by the firing the laser  20  toward the sample. In particular, the current  230 C may be determined based on a measurement of the voltage  201 V response to the current  230 C passing through the resistor  201 . 
     Moreover, the operations may include firing (Block  412 ′- 1 ) the laser  20  toward a blank slide that is free of any samples, and measuring (Block  412 ′- 2 ), via the resistor  201 , any current generated by the firing the laser  20  toward the blank slide, before the firing (Block  412 ′- 3 ) of the laser  20  toward the sample. For example, the operation(s) of Block  412 ′- 2  may include determining whether a measurable current generated by the firing (Block  412 ′- 1 ) the laser  20  toward the blank slide passes through the resistor  201 . In some embodiments, the respective measurements/results of the operations of Block  412 ′- 4  and Block  412 ′- 2  may be compared to determine the magnitude/impact of (a) ionization of a sample relative to (b) firing on a blank slide. For example, the operations of Block  412 ′- 4  and Block  412 ′- 2  may measure first and second electrical responses (e.g., voltage responses), respectively, by the resistor  201 , which may then be compared with each other and/or with predetermined value(s). In the case of the blank slide, as an electrical response may not be measurable, the absence of a measurable electrical response may be detected. Moreover, in some embodiments, the operation(s) of Block  412 ′- 1  (and/or Block  412 ′- 2 ) may be performed after the operation(s) of Block  412 ′- 3  (and/or Block  412 ′- 4 ). 
     Referring to  FIG.  4 E , the charged particles described with respect to  FIG.  4 B  may be the ions  230 I. As shown in  FIG.  4 E , the operation(s) of Block  412 ′ of  FIG.  4 B  may include determining (Block  412 ′-B) a quantity of the ions  230 I generated in the chamber  210 , based on a comparison (Block  412 ′-A) of the measured current  230 C with a predetermined value. The operations of  FIG.  4 E  may be performed either in addition to, or as an alternative to, the operations of  FIG.  4 D . 
       FIG.  5 A  illustrates a graph of oscilloscope traces for the instrument  10  firing on a blank slide. As shown in  FIG.  5 A , the response  501 A of the CVR voltage  201 V is flat (i.e., not measurable or noticeable) when firing on a blank slide. 
       FIG.  5 B  illustrates a graph of oscilloscope traces for the instrument  10  firing on the sample slide  230  having samples thereon. In this example, the instrument  10  is firing on samples of ATCC 8739 E. coli. As shown in  FIG.  5 B , the response  501 B of the CVR voltage  201 V is measurable/noticeable when firing on the samples. This stands in contrast with the flat response  501 A when firing on the blank slide in  FIG.  5 A . 
       FIG.  6    illustrates a perspective view inside the chamber  210  of  FIGS.  2 A and  2 B . This view illustrates the sample plate  230 , as well as the extraction plate  221  and the back bias plate  222 . 
     In some embodiments, the sample(s) on the sample plate  230  may include a biosample from a patient, and analysis of the sample can be carried out by the instrument  10  to identify whether a defined protein or microorganism, such as bacteria, is in the sample for medical evaluation of the patient. For example, the instrument  10  may be a mass spectrometer  10 M, and the analysis can identify whether any of about 150 (or more) different defined species of bacteria is in a sample, based on obtained spectra. The target mass range can be between about 2,000-20,000 Dalton. 
       FIG.  7    illustrates a block diagram of a resistor  201  in communication with processor(s)  270  and a laser source  20 LS for the calibration of laser energy and/or laser focusing. The processor(s)  270  may receive/process data/signals resulting from an electrical response by the resistor  201  to current generated by light from the laser  20 LS, and the processor(s)  270  may responsively control the laser  20 LS to adjust its laser energy and/or laser focus. The combination/communication of the processor(s)  270  with the laser  20 LS and the resistor  201  to control calibration of the laser  20 LS may provide a laser calibration system  770 C. Moreover, as described herein, the resistor  201  may be coupled to a power supply  202 , which may also be controlled by the processor(s)  270 . 
       FIG.  8    illustrates a flowchart of example method(s) for the calibration of laser energy and/or laser focusing. The method(s) may including coupling (Block  810 ) the resistor  201 , which is external to the vacuum chamber  210 , to current (e.g., the charged-particle current  230 C) that is generated inside the vacuum chamber  210  by light  20 L from the laser  20 LS. Accordingly, the term “coupling,” as used herein with respect to the resistor  201  and current, may refer to firing the laser LS at a target  230 T that is in the vacuum chamber  210  to generate current. Moreover, the method(s) may include adjusting (Block  830 ) the laser energy and/or the laser focus of the laser  20 LS, in response to a measurement (Block  820 ) of an electrical response, such as a voltage  201 V response, by the resistor  201  to the current. For example, the processor(s)  270  may compare a measured electrical response with a predetermined value (e.g., a threshold value or range), and perform the adjusting (Block  830 ) in response to deviation from the predetermined value. 
     The present invention advantageously provides for directly measuring the ion current  230 C generated from a sample. Conventional systems, by contrast, may only provide indirect feedback about ion current based on the intensity of peaks in mass spectra. Accordingly, in conventional systems, if no mass spectra are being generated, it may be difficult to determine whether ions are being generated, arriving at a detector, and/or resulting in an output signal by a detector. The measurement of the current  230 C by the present invention, however, may be performed when no mass spectra are generated. 
     The present invention also advantageously provides for measuring the ion current  230 C without requiring additional hardware (e.g., additional diagnostic hardware) inside the chamber  210 . Rather, any additional hardware (e.g., the resistor  201 , the power supply  202 , and the switches  201 S,  221 S, and  222 S) used to implement the methods (e.g., as a diagnostic) of the present invention for the instrument  10  can be external to the chamber  210 . 
       FIG.  9 A  illustrates Safe High Voltage (SHV) vacuum feedthroughs  910  that can be used with the instrument  10 . For example, the SHV feedthroughs  910  may be PASTERNACK® PE4500 SHV jack bulkhead hermetically sealed terminal connectors. In some embodiments, one of the feedthroughs  910  may be an extraction pulse SHV feedthrough and another of the feedthroughs  910  may be a back bias SHV feedthrough. 
       FIG.  9 B  illustrates an SHV patch cable  920  that can be used with the instrument  10 . For example, the SHV patch cable  920  may be connected between a resistor measurement box  201  and the atmospheric side of a back bias SHV feedthrough  910  to connect one side of the resistor  201  to the back bias plate  222 . 
     The following is one non-limiting example of the methods/diagnostic described herein. To assist in the troubleshooting of mass spectrometry instruments/systems, the following procedure was developed to test the occurrence of ionization at a sample. An underlying principle of the procedure involves using a charge collection plate and a CVR. Existing connections of the instrument/system are modified so that a lower removable portion of the ion optics of the instrument/system may facilitate the diagnostic. The diagnostic may include the following operations: 
     1. Set the laser optics positions to those specified in the instrument/system tuning procedures. 
     2. Turn off all high voltages, to protect against damaging the instrument  10 . 
     3. Vent the vacuum system. 
     4. Inside the vacuum chamber  210 , disconnect all cables attached to the removable ion optics  220 , with the exception of the back bias and extraction pulse cables. The remaining connections should not go through any voltage dividers in the vacuum chamber  210 . Moreover, ensure that unused cables are not shorted to a wall of the vacuum chamber  210 . 
     5. Remove the deflector portion  223  of the ion optics assembly  220 . Leave the lower portion of the ion optics assembly  220  in place. 
     6. Close the door and start pumping down the vacuum chamber  210  to operation pressure (less than 3×10 −6  Torr). 
     7. Disconnect the extraction pulse cable from the atmospheric side of the extraction pulse Safe High Voltage (SHV) feedthrough  910 . 
     8. Attach a shorting plug to the atmospheric side of the extraction pulse SHV feedthrough  910 . This grounds the extraction plate  221 . 
     9. Disconnect the back bias cable from the atmospheric side of the back bias SHV feedthrough  910 . 
     10. Connect an SHV patch cable  920  between a resistor measurement box  201  and the atmospheric side of the back bias SHV feedthrough  910 . This connects one side of the resistor  201  (e.g., a 10 kV, 1 Watt, 10 MΩ+/−5% resistor) to the back bias plate  222 . 
     11. Connect a DC power supply  202  capable of −200 V to the remaining side of the resistor measurement box  201 . Note that the polarity is negative for the inner conductor. It may be desirable to use a power supply that can been controlled via a Graphical User Interface (GUI). A benchtop power supply, however, may be used. In some embodiments, a power supply of the detector  250  may be used. An adapter or a different termination may be used with the power supply of the detector  250 , as this power supply may be terminated in Miniature High Voltage (MHV). 
     12. Connect standard 10× oscilloscope probes  310  rated for &gt;300 V to either side of the resistor  201  in the measurement box. The corresponding channels on the oscilloscope may be Alternating Current (AC) coupled. 
     13. On the oscilloscope, create a math function to subtract the two probe voltages. This creates a differential voltage measurement (the CVR voltage  201 V) across the resistor  201 . 
     14. Connect a cable to the laser sync output of the laser  20 . This may be achieved via a test point or connector on the circuit boards. For example, a connector of a timing board may be used. 
     15. Set the oscilloscope to trigger on the leading edge of the laser sync signal. This is shown as a falling-edge trigger in  FIG.  5 A , but may be different depending on electronics design. 
     16. Insert a blank slide with no samples into the instrument  10  and pump down to operating pressure. 
     17. Set all high voltages in the instrument  10  to be 0 V during acquisition, to protect against damaging the instrument  10 . 
     18. Set the DC power supply  202  to −200 V. This may be easier to set with no averaging on the oscilloscope. 
     19. Set the oscilloscope to average  64  events. The signal may be very noisy without averaging. The averaging should make the signal more distinguishable from noise. 
     20. Begin firing the laser  20  on the slide and raster, if possible. The laser energy at the slide should be approximately 5 microJoules (μJ). This was achieved with a laser power of 20 μJ from the laser  20 . The 5 μJ value is based on measurements of 1.5 μJ at the sample for 6 μJ from the laser  20 . When using a blank slide, the math function representing the differential voltage  201 V across the resistor  201  should not change at a laser trigger event, as shown in  FIG.  5 A . In  FIG.  5 A , channel  1  is the voltage of the DC power supply  202 , channel  2  is the laser sync event, channel  3  is the voltage probe  310  on the power supply  202  side of the resistor  201 , and channel  4  is the voltage probe  310  on the vacuum chamber  210  side of the resistor  201 . 
     21. Discontinue firing on the blank slide. 
     22. Replace the blank slide with a full slide of ATCC 8739 E. coli and pump down to operating pressure. These samples can be from either suspension or manual deposits. In some embodiments, fresh samples may be suspended in matrix. 
     23. Set all high voltages in the instrument  10  to 0 V during acquisition, to protect against damaging the instrument  10 . 
     24. Set the DC power supply  202  to −200 V. This may be easier to set with no averaging on the oscilloscope. 
     25. Set the oscilloscope to average  64  events. The signal may be very noisy without averaging. The averaging should make the signal more distinguishable from noise. 
     26. Begin firing the laser  20  on the slide and raster, if possible. The laser energy at the sample should be approximately 5 microJoules (μJ). This was achieved with a laser power of 20 μJ from the laser  20 . The 5 μJ value is based on measurements of 1.5 at the sample for 6 μJ from the laser  20 . When using a slide with samples, the math function representing the differential voltage  201 V across the resistor  201  should change by approximately 10 milliVolts (mV) during a laser trigger event, as shown in  FIG.  5 B . 
     This change in voltage on the CVR  201  is proportional to the ion current  230 C collected in the instrument  10  via Ohm&#39;s law. In  FIG.  5 B , channel  1  is the voltage of the DC power supply  202 , channel  2  is the laser sync event, channel  3  is the voltage probe  310  on the power supply  202  side of the resistor  201 , and channel  4  is the voltage probe  310  on the vacuum chamber  210  side of the resistor  201 . 
     27. Discontinue firing on the E. coli samples. 
     28. Remove the slide of E. coli samples from the instrument  10 . 
     In the figures, certain layers, components, or features may be exaggerated for clarity, and broken lines illustrate optional/removable features or operations unless specified otherwise. The terms “FIG.” and “Fig.” are used interchangeably with the word “Figure” in the application and/or drawings. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the invention to those skilled in the art. 
     It will be understood that, although the terms “first,” “second,” etc. may be used herein to describe various elements, components, regions, layers, and/or sections, these elements, components, regions, layers, and/or sections should not be limited by these terms. These terms are only used to distinguish one element, component, region, layer, or section from another region, layer or section. Thus, a “first” element, component, region, layer, or section discussed below could be termed a “second” element, component, region, layer, or section without departing from the teachings of the present invention. 
     Spatially relative terms, such as “beneath,” “below,” “bottom,” “lower,” “above,” “upper,” and the like, may be used herein for ease of description to describe one element or feature&#39;s relationship to another element(s) or feature(s) as illustrated in the figures. It will be understood that the spatially relative terms are intended to encompass different orientations of the device in use or operation in addition to the orientation depicted in the figures. For example, if the device in the figures is turned over, elements described as “below” or “beneath” other elements or features would then be oriented “above” the other elements or features. Thus, the example term “below” can encompass orientations of above, below and behind. The device may be otherwise oriented (rotated 90° or at other orientations) and the spatially relative descriptors used herein interpreted accordingly. 
     The term “about” refers to numbers in a range of +/−20% of the noted value. 
     As used herein, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless expressly stated otherwise. It will be further understood that the terms “includes,” “comprises,” “including,” and/or “comprising,” when used in this specification, specify the presence of stated features, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and/or groups thereof. It will be understood that when an element is referred to as being “connected” or “coupled” to another element, it can be directly connected or coupled to the other element or intervening elements may be present. As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items. Moreover, the symbol “/” has the same meaning as the term “and/or.” 
     Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of this specification and the relevant art and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein. 
     In some embodiments, the mass spectrometer  10 M is configured to obtain an ion signal from a sample that is in a mass range of about 2,000 to about 20,000 Dalton. 
     The term “sample” refers to a substance undergoing analysis and can be any medium within a wide range of molecular weights. In some embodiments, the sample is being evaluated for the presence of microorganisms such as bacteria or fungi. The sample, however, can be evaluated for the presence of other constituents, including toxins or other chemicals. 
     The term “table top” refers to a relatively compact unit that can fit on a standard table top or counter top or occupy a footprint equivalent to a table top, such as a table top that has width-by-length dimensions of about 1 foot by 6 feet, for example, and which typically has a height dimension that is between about 1-4 feet. In some embodiments, the instrument/system resides in an enclosure or housing of 28 inches−14 inches (W)×28 inches−14 inches (D)×38 inches−28 inches (H). The flight tube  240  may have a length of about 0.8 meters (m). In some embodiments, longer or shorter lengths may be used. For example, the flight tube  240  may have a length that is between about 0.4 m and about 1 m. 
     The foregoing is illustrative of the present invention and is not to be construed as limiting thereof. Although a few example embodiments of this invention have been described, those skilled in the art will readily appreciate that many modifications are possible in the example embodiments without materially departing from the novel teachings and advantages of this invention. Accordingly, all such modifications are intended to be included within the scope of this invention. Therefore, it is to be understood that the foregoing is illustrative of the present invention and is not to be construed as limited to the specific embodiments disclosed, and that modifications to the disclosed embodiments, as well as other embodiments, are intended to be included within the scope of the invention.