Scriptorium Update: Ion Mobility Calculator

A brief, condensed tutorial of IMS calculations and simulation is provided in the following jupyter notebook. This example code is meant to serve as an introduction to the topic and provide tractable to enable correct reporting of ion mobility measurements.

Continued updates will pushed to the CRG github account including any changes to the Excel version of the notebook.

Quantifying Proton-Bound Heterodimer Association Energies from Drift Time Shifts

Previously, we reported an approach to quantify the energetics of association between neutral drift gas modifiers and two common chemical warfare agent degradation species by a combination of experimental drift time shift data as well as computational modeling in collaboration with Chris Hogan at the University of Minnesota. As a continuation of this research in conjunction with Dr. Hogan, we are pleased to report the acceptance of our article for publication in The Journal of Physical Chemistry A entitled, “Deducing Proton-Bound Heterodimer Association Energies from Shifts in Ion Mobility Arrival Time Distributions.” This report describes the Gibbs free energy, enthalpy, and entropy changes as propanol is dimerized with a homologous series of alkylphosphonic acids (methyl-, ethyl-, and propylphosphonic acids) and its conformation with the Kelvin-Thomson-Raoult model.

Segmented Quadrupole — PCB Edition

Recently we’ve been working on the design and construction of a new instrument build centering around a quadrupole mass spectrometer as a detector for ion mobility spectromety. The primary motivation is to monitor the arival time distributions (ATDs) for specific ions without the duty cycles limitations of TOF system. In many ways this may concept may be counter-intuitive, however, though TOF systems are quite fast (operating into the kHz range), if they are used as sampling devices for drift tube IMS separations cycle times in that approach 10 kHz only allow sampling of the IMS domain every 100 microseconds. When placed into context of higher resolution IMS experiments such sampling rates are largely inadequate for capturing enough points across the ATD. While we surely have not solved this problem fully, the current build needs to shuttle the any ion packets efficiently towards the detector. Stated differently, any delay in getting ions to the detector aids contributions to peak widths from diffusion–this we want to minimize. Below are a few sketches of the target build in Solidworks and the newly arrived segmented quadrupoles. Key things to remember is that this design is not aimed at a resolving quadrupole but rather one focused on ion transmission. Also, the great technical notes at Ardara Technologies would suggest that a simple rectilinear quadrupole would be sufficient for ion trasport but we simply wanted to explore this possibility.

Building upon some of the ideas at the Rowland Institute we had some of the segments comprising the higher pressure quad manufactured along with the necessary coupling board. The coupler depicted corresponds to the one-half of the RF signal needed to power the setup. Stay tuned for the results on the implementation. For those interested in the actual files (still a work in progress) hop on over to github for the files.

Schematic of the segmentic PCB ion guide.
Top view of the segmented quad. Things to note include the 0.01″ teflon spacer between boards. The tabs are not ideally located (oversight on beta design) but in newer version this is corrected. The clamp is simply used to simulate the compression necessary to hold the setup together.
Side view of the assembly. Notice that the PCB routing does not produce a smooth surface, however, we expect the ion transmission characteristics to be largely unaffected by this manufacturing by-product.
Slotted coupling board illustrating the concept behind the assembly and electric signal connections.

Non-Contact, Trace Tributyl Phosphate Vapor Analysis

Following our initial experiments using ion trap mass spectrometry and atmospheric flow tube sampling (AFT-MS) for alkylphosphonic acid detection, we have applied a similar approach to the quantitation of tributyl phosphate in solution by analysis of headspace vapor. We are pleased to present this research, performed in collaboration with Robert Ewing from Pacific Northwest National Laboratory, as an accepted publication in Talanta entitled, “Ambient Vapor Sampling and Selective Cluster Formation for the Trace Detection of Tributyl Phosphate via Atmospheric Flow Tube Mass Spectrometry.” In this article, AFT-MS is shown to successfully quantitate tributyl phosphate down to tens of ppb in solution. Furthermore, analytical selectivity and quality control accuracy was enhanced by the introduction of specific dopant molecules.

Ambient Alkylphosphonic Acid Vapor Detection and Ion Traps

Atmospheric flow tube-mass spectrometry (AFT-MS) first emerged in 2012 as an ambient vapor sampling technique developed by Ewing et al. and applied to the sensing of trace quantities of RDX molecules clustered with nitrate ions. This iteration of AFT-MS used selected-ion monitoring (SIM) during analysis via a triple-quadrupole mass spectrometer and subsequently has been applied to vapor analysis of other explosives adducted with nitrate as well as positively-charged organophosphorus species clustered with amines as proton-bound dimers. Building upon these initial AFT-MS experiments, we have recently applied the atmospheric flow tube ionization method to the detection of alkylphosphonic acids from methanol solution headspace and adducted with nitrate and nitrate-nitric acid species via linear ion trap mass spectrometry. This was performed in an effort not only to demonstrate the application of ion trap MS systems with AFT-MS, but also to characterize the gas-phase ion chemistry of a homologous series of alkylphosphonic acids including methylphosphonic acid (MPA), which is an environmental pollutant and hydrolysis product of some chemical agents. Our article, “Characterization of Alkylphosphonic Acid Vapors Using Atmospheric Flow Tube-Ion Trap Mass Spectrometry,” can be found in Rapid Communications in Mass Spectrometry.

IM-MS Assessment of Cobalt-Glycan Heterodimers

Continuing along our previous work to characterize certain cationized glycans with a variety of metals and with cobalt to enhance UV photon absorption, we are pleased to show our effort to demonstrate the formation of heterodimeric cobalt-glycan adducts in published form. Now appearing as an online-first article in Journal of the American Society for Mass Spectrometry, our paper “Assessment of Dimeric Metal-Glycan Adducts via Isotopic Labeling and Ion Mobility-Mass Spectrometry” presents how important ion mobility separations are for tandem MS experiments performed on divalent metal-glycan adducts. Without the ability to use drift times to distinguish which precursor produced which fragment ions, component fragments from a heterodimeric adduct of two isomers cannot be deconvoluted. Specifically, the potential for isomers to form doubly-charged heterodimers–that are then dissociated into component fragments–will essentially create a scenario where chimeric fragmentation spectra are produced.

Open Source IMS Initiative Update


Following up on previous post, we’ve finally released a major update to the Open Source IMS Initiative.  Appearing now in Hardware X we detail a new modular IMS design that is extremely flexible.  Three of our ASMS 2018 posters feature data from these system and the are proving an invaluable new tool to our research infrastucture.  Though the current systems are limited to lower temperature operation (i.e < 120 °C),  the designs are readily adapted to Rogers material which is quite robust well above 200 °C.  Another key adaptation making this design tractable is the new ion shutter design which uses 3 grids to create a set of well defined ion pulses.  Though the BN-gates are attractive in that the physical structure is in a single plane, their construction is an art.  Moreover, the fields established by the BN gates are also, by no means, fully planar.  With the new design we can achieve that smooth field in the region surrounding the ion gate and still get extremely small ion gate pulse widths (i.e < 20 μs).  If you are interested in some of the core details or have suggestions for improvement, come find us on github:


Ion Gates?! Where we’re going we don’t need ion gates!

Ion gating remains a critical aspect of drift tube IMS experiment and a range of clever approaches have been used the past.  However, most techniques use a physical grid to modulate the ion beam. In collaboration with Steve Kenyon and Keith Gendreau we’ve adapted a modulated x-ray source to printed circuit board IMS.  Though there is still room for improvement, the initial results look quite promising.  Interestingly, because the source is now located orthogonal to the drift axis, a new term is added to the descriptors of peak width.  What we’re most excited about, however, is the fact that because we no longer have a physical ion gate, some of the capacitive coupling during the pulsing of a standard ion gate is now effectively eliminated–enter artifact-free multiplexing…

Recent Publication: Mobility Separation and UVPD of Co-Adducted Tetrasaccharides


Ultraviolet photodissociation (UVPD) has had its application directed primarily at biomolecule analysis, but with a common drawback of low fragment abundances. We encountered this same problem with UVPD of two sodiated isomeric glycans, but found a significantly higher fragment yield from the cobalt adducts of those same tetrasaccharides. An additional bonus was that the cobalt adduction increased the resolution of the isomers from no discernible mobility separation as sodium adducts to a resolution of 0.78. This allowed us to use UVPD for fragmenting a mobility separated mixture of the two glycans, which benefited from the higher fragment yield of the cobalt adducts.

Paper Link:

Recent Publication: Enhanced Mixture Separations of Metal Adducted Tetrasaccharides


Using a combination of Fourier transform ion mobility and ion trap mass spectrometry Kelsey demonstrated the degree to which different metal cations were able to enhance isomer separations across a set of tetrasaccharides.  While full resolution was not achieved for the full set of 5 isomers this work demonstrates the current state of the art for true isomeric mixture separations using IMS.  Another interesting aspect of this work was the observation of metal cation bound dimers.  Though we couldn’t tell whether they were homo or heterodimers we’ve now obtained a deuterated set of isomers which will help to answer that question.

Paper Link:


Open-Source, Modular Approaches to Ion Mobility Spectrometry

Pulse_Comp_v3Outside of an ionization source and a Faraday plate, a drift tube IMS system is fundamentally comprised of 5 primary components:

  • Reaction/Drift Cell
  • Ion Gate
  • Gate Pulsing Electronics
  • Current to Voltage Converter
  • Data Acquisition System (DAQ)

Within the IMS research community hardware and DAQ solutions are often custom and rarely replicated exactly. In an effort to address this knowledge and resource gap, the links posted below outline a range of solutions to the construction and operation of research-grade ion mobility spectrometers.  It is our sincere hope that this information will be useful to other research groups and encourage others to make suggestions and improvements.  The github links, including those from GAA Custom Engineering are found below:

Ion Gate Pulser

Current to Voltage Converter

WiPy DAQ System and GUI

The most recent poster presented ISIMS 2016 in Boston, MA can be found here: Clowers_ISIMS_2016_v5.

Fourier Transform Ion Mobility-Ion Trap Mass Spectrometry


We are pleased to report the publication of our work outlining the effective coupling of a drift tube IMS system with an ion trap mass spectrometer.  Compared to previous implementations (see our 2005 publication) we have dramatically improved the IMS duty cycle by encoding the mobility information in the frequency domain.  Using this Fourier approach we can cover the full mobility spectrum in a fraction of the time that is typically required for a signal averaging technique.  Perhaps most impressive from our perspective, is the ease of implementation.  It is truly plug ‘N play with no hardware synchronization required. If anyone is interesting in more details regarding the pulsing hardware and parameters, you know where to find us.

Abstract: Historically, high pressure ion mobility drift tubes have suffered from low ion duty cycles and this problem is magnified when such instrumentation is coupled with ion trap mass spectrometers. To significantly alleviate these issues, we outline the result from coupling an atmospheric pressure, dual-gate drift tube ion mobility spectrometer (IMS) to a linear ion trap mass spectrometer (LIT-MS) via modulation of the ion beam with a linear frequency chirp. The time-domain ion current, once Fourier transformed, reveals a standard ion mobility drift spectrum that corresponds to the standard mode of mobility analysis. By multiplexing the ion beam, it is possible to successfully obtain drift time spectra for an assortment of simple peptide and protein mixtures using an LIT-MS while showing improved signal intensity versus the more common signal averaging technique. Explored here are the effects of maximum injection time, solution concentration, total experiment time, and frequency swept on signal-to-noise ratios (SNRs) and resolving power. Increased inject time, concentration, and experiment time all generally led to an improvement in SNR, while a greater frequency swept increases the resolving power at the expense of SNR. Overall, chirp multiplexing of a dual-gate IMS system coupled to an LIT-MS improves ion transmission, lowers analyte detection limits, and improves spectral quality.

Dr. Clowers Recognized for Early Career Achievement

In the Spring Semester of 2015, Dr. Clowers was recognized within the College of Arts and Sciences at Washington State University for Early Career Achievement.  The College of Arts and Sciences celebrated achievements in teaching, research, and mentoring at its third annual Appreciation and Recognition Social on April 22, 2015.  Dr. Clowers was one of the nineteen faculty and staff, and six graduate students from across the college who were honored for their contribution to the WSU community and their commitment to excellence.


Live from Fulmer Hall: Waters G2

We are pleased to announce the unpacking and, more importantly, the successful pump down of the G2.  Combined with a new UPLC unit we anticipate this instrument playing a large role in future metabolomics work in our laboratory. Kudos to Justin Chang from Waters for executing the pump down sequence like a champ.  IMG_2148



IMS – Ion Trap Equipped with UV Photofragmentation


Comparison of CID and UV Photodissociation of Leucine Enkephaline Acquired at WSU.


In early 2015 the research group is pleased to bring the next generation ion mobility-ion trap system online.  This system is equipped with two ion gates which allows the speed of the IMS to be effectively coupled to the slow scan speeds of traditional ion trapping experiments.  Though not as fast as tradition IMS-TOF configurations, this experimental setup does allow multiple stages of CID and alternative modes of fragmentation such as UV and IRMPD.  Another unique feature of this IMS system is that it can obtain IMS spectra using a standard Faraday plate and/or the LTQ.

Additional photos of the initial setup and UV beam line:


The ExcellIMS Dual Gate System smoothly mates to the LTQ.


Though a little difficult to see the IMS tube actually uses a square drift tube design with a nice set of BN gates.


Fully functional Dual-Gate IM-LTQ system.




193 nm Excimer Beam Line


We Have Ignition on Ion Engine #1

First Data AcquiredThe Clowers Research Group is now live.  Reporting in are the background ions from ionized air measured using a residual quadrupole gas analyzer and the LeCroy “Panzer” oscilloscope.  These data are to help monitor background gases in the high vacuum chamber (not shown) and provide diagnostic support for gases ionized by the excimer laser (also not shown).  With a little luck, laser beams are next week.  Stay tuned…


PCB Tools and Gerber Viewer

Though seemingly outside the realm of chemistry, electronics lie at the heart of many experimental disciplines as all rely ability to make accurate and reproducible measurements.  An unfortunate byproduct of this requirements is often the reliance on outside sources–just look at your oscilloscope should there be any questions.  In an effort to minimize this reliance an maintain a solid knowledge base within the laboratory we often use the following tools for simple circuits:

Eagle — Great, free board editing and layout tool

Gerbv* — Simple, cross-platform gerber viewer

*for those working in OSX ♠hombrew♠ must be installed prior to installing gerbv. Beware, homebrew will change your life.