Creating an Integrated and Flexible Control Solution for Mass Spectrometer Systems Using PXI Hardware and LabVIEW

Ryan Danell, Danell Consulting

"This solution has accommodated all possible experiment configurations desired on an ion trap mass spectrometer. Its performance and capabilities have equaled or surpassed those available on commercial instruments. The flexibility afforded by the NI PXI hardware and LabVIEW software ensures that the system can grow as experimental needs in this field change in the future."

- Ryan Danell, Danell Consulting

The Challenge:

Creating an end-to-end control, acquisition, and analysis system for research-grade ion trap mass spectrometer systems that can accommodate experiments of varying complexity and sophistication.

The Solution:

Using NI LabVIEW software and a diverse selection of NI data acquisition (DAQ) hardware to build a modular, flexible, high-performance, fully integrated solution to handle experiments of varying length with selectable time-step resolution.

Danell Consulting Inc. specializes in scientific consulting, particularly instrument control, data analysis, and simulation. Our primary focus is on mass spectrometry and we specialize in equipping experimenters with custom hardware, software, and data analysis algorithms to help them mine through the large quantities of data collected in labs around the world. While many commercial mass spectrometer systems are available, researchers often need tailor-made systems. Through hardware and software design projects at Harvard University and Johns Hopkins University, we developed a flexible, full-featured software- and hardware-based control architecture for ion-trap-based mass spectrometer systems. This platform has been used to study clusters of biological and inorganic species in the gas phase and to control and test a mass spectrometer that will be an integral instrument on a rover destined for Mars.


Ion Trap Mass Spectrometry

Ion trap mass spectrometry uses an electric field to trap ionized molecules in a vacuum. RF voltage applied to specially shaped electrodes creates the field. The trapped ions can be further manipulated through the application of additional RF and DC potentials to the electrodes. It is the control and manipulation of the trapped ions that make ion traps so versatile and popular in chemical research. The masses of the ions are determined as they are sequentially scanned as they exit the trap and detected with an electron multiplier tube. The multiplier output is amplified and converted to a voltage that is digitized by an ADC interfaced to a computer. Complete control of an ion trap mass spectrometer also requires manipulation of various RF and DC potentials that control the ion source, which creates and transfers the ions into the trap. As the trapping experiment occurs over time, a complex series of electrode potentials and data collection events must be controlled in a highly synchronized manner.


Benefits of Modular PXI Hardware

While commercial instruments typically use proprietary electronics to supply the necessary signals and inputs to control an instrument, it is possible to use stand-alone hardware to control an ion trap. We can interface laboratory-grade power supplies, waveform generators, and scopes with amplifiers, delay generators, and other small custom circuits to build a complete control system. However, this solution requires extensive modification of individual components to achieve synchronization, and the researcher may still be significantly limited in the types of experiments they can conduct. PXI hardware integrated into a single chassis (or multiple connected chassis) alleviates all of the limitations of stand-alone hardware and provides a wider range of connectivity and synchronization options. We can easily modify hardware configurations through software without rewiring connections and setting up individual components. We can easily add more capabilities to the system by introducing more PXI modules – a feature we have used many times in this project already. Current systems use multifunction data acquisition modules for analog outputs (lens controls), digital outputs (triggers), analog input (ion signal), dedicated analog output PXI modules, and arbitrary waveform generator PXI modules.




One example configuration uses an NI PXI-6229 multifunction DAQ module to provide analog input for the ion signal, digital output for system triggers, and analog outputs to control lens power supplies; and an NI PXI-6723 analog output module to provide additional correlated analog outputs for the remaining power supplies. We synchronize two NI PXI-5412 arbitrary waveform generators – one supplies the fundamental RF signal used to trap the ions and the other generates the specialized waveforms used to manipulate the trapped ions.


We have easily implemented the ability to phase-lock and phase-shift two waveforms with the PXI architecture. Phase control is critical for high-performance ion trap operation. By using two waveform generators running on the same PXI clock and synchronized through the PXI backplane, we can implement complete control over the phase relationship of these signals using a few simple software routines. Normally this would require advanced stand-alone equipment and/or an additional delay generator to accomplish the same task.


Integration and Synchronization with Software

The complete integration of the DAQ hardware into LabVIEW made it the obvious choice for developing our control software. With the many capabilities of LabVIEW, we efficiently produced a high-quality control application and could still modify the application when we needed to change the experiment. In addition to experiment control, we built data analysis and processing features to help users easily interpret the data collected. Through the exclusive use of dialog controls in the UI design, users get a familiar interface that is polished, professional, and easy to learn.




As previously mentioned, an ion trap mass spectrometer relies on precise timing of events that dictate the overall experiment operation. Various portions of the experiment demand different resolution over a range of measurement times. Some experiments are meant to run quickly (tens of milliseconds), whereas others can take longer (tens of seconds). We set up the hardware and built the software to reconfigure the boards during the experiment to alter the time resolution and take full advantage of the capabilities of the DAQ modules while using minimal system resources. With LabVIEW support of object-oriented programming, we can add advanced features to the software in an efficient manner. For example, the user can reconfigure individual portions of the experiment while it is running and have those specific outputs and/or waveforms updated instantly and applied in subsequent mass scans.



We have used this hardware and software architecture on several different instruments encompassing a range of experiment types and configurations. It has accommodated high-repetition rate experiments with only a few milliseconds of dead time between repetitions while data is written to disk. Very complex experiments have been effortlessly set up using multiple waveform application steps for advanced ion control and manipulation.


Overall, this solution has accommodated all possible experiment configurations desired on an ion trap mass spectrometer. Its performance and capabilities have equaled or surpassed those available on commercial instruments. The flexibility afforded by the NI PXI hardware and LabVIEW software ensures that the system can grow as experimental needs in this field change in the future.


Author Information:

Ryan Danell
Danell Consulting
United States
Tel: (252) 258-7569

Figure 1. UI for the Data Acquisition Portion of the Software
Figure 2. Basic Ion Trap Experimental Sequence Showing Example Signals
Figure 3. Block Diagram of Hardware Setup and Interconnectivity
Figure 4. Mass spectrum of polycyclic aromatic hydrocarbons (PAHs) ionized via laser desorption ionization. The laser is triggered via a digital output from a PXI module. The inset shows the resolution obtained for the isotopes of Pyrene.