Organophosphorus Proton Affinities from AFT-MS and Kinetic Method with Computational Values
After applying the atmospheric flow tube-mass spectrometry approach to ambient vapor detection of phosphonic acids and tributyl phosphate, we observed that few organophosphorus compounds have reported proton affinities in the literature. Phosphonate species that are structurally similar to chemical warfare agent simulants in particular are valuable to characterize, which is… Continue reading
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… Continue reading
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… Continue reading
IMS Spectral Simulator: Arduino Edition
TL/DR — Code and wiring diagram to output a simulated spectrum WITH noise on a specified microcontroller output pin. Requires hardware interrupts which simulate a gating pulse. When developing new approaches to signal processing or simply designing a new data acquisition system, having a reasonable reflection of the target signal… Continue reading
Determining Proton Affinities using psi4
This is the 3rd post in a series outlining a workflow using freely available computational chemistry resources with python interfaces to evalute properties of gas-phase ions. A cursory search illustrates that there are a variety of computational packages with a direct python interface but interestingly, not all of these packages… Continue reading
Geometry Optimization in Python
This is the second post in a series aiming at generating a range of candidate structures for evaluation in the context of molecular modeling in the field of ion mobility spectrometry. In a previous post, the use of rdkit to generate structures was introduced. However, closer inspection of the code… Continue reading
Conformational Searching using Python
This is the first of a series examining the use of python to generate candidate structures of molecules. These conformations may serve a variety of functions, though our particular purpose is to identify candidates for additional optimization and ultimate use in ion mobility modeling experiments. After considering a range of… Continue reading
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… Continue reading
Congrats to Zhihao Yu for a successful dissertation defense!
Updated IMS Worksheet — 2018
For those that are interested, here is the spreadsheet used in the ASMS 2018 short course. Thank Dr. Bill Siems if you see him. Ion Mobility Cal v3 Continue reading
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… Continue reading
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… Continue reading
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… Continue reading
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… Continue reading
Congrats to Austen Davis for a Successful Disseration Defense!
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… Continue reading
Animation: Improving Rp by Increasing DT Cell Length
Austen has recently assembled an animation demonstrating the effect of increasing drift tube length on resolving power, calculated from peak width contributions from diffusion and gate pulse width. Click the image to view. Continue reading
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… Continue reading
Open-Source, Modular Approaches to Ion Mobility Spectrometry
Outside 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… Continue reading
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… Continue reading
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.… Continue reading
IMS Short Course Worksheet
For those that are interested, here is the spreadsheet used in the ASMS 2018 short course. Thank Dr. Bill Siems if you see him. Ion Mobility Cal v3 Continue reading
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… Continue reading
Waters G2 at WSU
Unboxing to commence in t-minus 6 days and counting… Continue reading
IMS – Ion Trap Equipped with UV Photofragmentation
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… Continue reading
Savitzky-Golay Smoothing GUI
In an effort to create a set of simple tools that are useful for data processing and realtime analysis of data we’ve been exploring a range of tools. Granted there are a number of canned solutions in existence (e.g. National Instruments), however, to avoid the long-term challenges of compatibility we… Continue reading
Venn Diagram Widgets
Generally, it is recommended to avoid qualitative measures when quantitative solutions exist. However, if the genuine need arises here are a list of useful Venn diagram widgets that may be found online: Quite Powerful: http://bioinformatics.psb.ugent.be/webtools/Venn/ Simple Solution: http://www.bioinformatics.lu/venn.php Downloadable: http://pcarvalho.com/patternlab/vennDiagram.shtml Continue reading
3D Printing CTC PAL Autosampler Trays
Recently, we brought two CTC PAL systems on-line in the group and in an effort to save a little bit of money* and explore the utility of 3D printing we engaged the engineering department at WSU to print out a sample trays that was compatible with the PAL system. Granted… Continue reading
Gantt Charts in Matplotlib
Love it or hate it, the lack of a tractable options to create Gantt charts warrants frustration at times. A recent post on Bitbucket provides a nice implementation using matplotlib and python as a platform. In order to expand the basic functionality a few modifications enable a set of features that… Continue reading
We Have Ignition on Ion Engine #1
The 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… Continue reading
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… Continue reading
Feynman Lectures Online
While many have heard of the legendary lecture series, few can claim to have actually read each one. Thanks to the folks at CalTech the barrier has now been lowered significantly. Click the mug for the TOC. Continue reading
XKCD-style Plots in Matplotlib
Now incorporated directly into the latest version of matplotlib (v1.3) here is a great alternative that brings some style to your plotting routines. I haven’t tried it out on plots with a huge number of points but I imagine it should work just fine. Below are some simple examples. Simple… Continue reading
Useful Links
Duviz: command line tool for disk usage visualization: duviz.py is a simple UNIX command line utility written in Python to visualize disk space usage. See it in action here:. I started writing it a couple of years ago (2009 according to the git commit log), but I just recently decided to make it more public. – http://stefaanlippens.net/duviz-command-line-tool-for-disk-usage-visualization
John Hunter Memorial Fund: John Hunter, author of Matplotlib, founding board member of NumFOCUS, husband to Miriam, and father to three daughters: Clara, Ava, and Rahel, was diagnosed with cancer in late July 2012 after returning from his keynote address at SciPy in Austin, TX. – http://numfocus.org/johnhunter/
tangle: Tangle is a JavaScript library for creating reactive documents. Your readers can interactively explore possibilities, play with parameters, and see the document update immediately. Tangle is super-simple and easy to learn. This is a simple reactive document. – http://worrydream.com/Tangle/
Measurement Basics: Tips and Tricks
Why Oscilloscope Bandwidth Matters: A big part my New Year’s Resolution to improve my overall design process was better testing. Better testing is an important part of better and more intentional design, but it means having tools that you can trust and that can consistently give you the results you need. – http://www.adafruit.com/blog/?p=23753