Reilly, Peter

Professional Experience

Feb. 1998 to 2010: Staff Scientist, Oak Ridge National Laboratory. Research has involved: characterization of aerosols by mass spectrometry; development of aerosol-base MALDI of biomolecules in an ion trap; mass spectrometry of bacteria, chemical weapons agents, explosives; isotope mass spectral analysis of single airborne particles; analysis of the formation of elemental carbon by hydrocarbon pyrolysis, formation of carbon nanotubes and carbon composites; digital ion trap development; development of miniature ion trap mass spectrometers; development of methods and instrumentation to extend the working range of mass spectrometry out to the billion Da range and beyond.

July 2010 to February 2023: Associate professor of chemistry, Washington State University. My group has increased the working range of mass spectrometers from roughly m/z 20,000 to m/z 1,000,000. My research is therefore focused on the development and applications of ultra high mass spectrometry. Application development will focus on the measurement of complex protein distributions, discovery of biomarkers, the interaction of proteins to form complexes with small and large molecules, DNA sequencing and much more. My group will also continue to develop digital waveform technology in the small and large molecule regimes.

February 2023 to present: Full professor of chemistry, Washington State University.  In collaboration with Gordon A. Anderson, we have developed a new form of digital waveform generator that produces rectangular waveforms with 1ppm or better duty cycle resolution with low (1ppm) waveform to waveform period jitter.  With it, we are able to access higher stability zones of ion trap and mass filter operation to simultaneously provide higher resolution and signal to noise.  Currently, through our collaboration, this waveform generator is being improved and tested.  Each factor of two improvement in waveform reproducibility yields the same improvement in accessible resolution and a disproportionate (~ x7) improvement in signal to noise.  My group is currently applying this waveform generator and higher stability zone analysis to native spray ionization of intact large proteins and complexes.

Group Goals

The overarching goal of our research is to extend the working range of mass spectrometers from roughly 20 kDa to the MDa range and beyond. We want to be able to provide resolved mass analysis for large intact proteins, complexes, RNA, DNA, and even viruses in low charge states.  Toward this end, our group has pioneered the theory, hardware, software, and methods of applying digital waveform technology to the analysis of large biomolecules and complexes.  Digital waveforms can not only be used to extend the mass range they provide new methods for performing mass analysis.  They can be used to convert an ordinary ion guide into a sophisticated ion trap or a digital mass filter that can provide better sensitivity and resolution by operating in higher stability zones.  It is our goal to spread this technology through collaboration with other academic groups and instrument manufacturers.  We are beginning to have success in this endeavor (see reference [3] below).

Publications

[1]  P. T. A. Reilly; A. P. Huntley, The Relationships Between Resolution, Dimensionless Stability, Pseudopotential Well Depth, Acceptance, and Transmission. Journal of The American Society for Mass Spectrometry 2021, submitted.

[2]  P. T. A. Reilly; S. Chakravorty; C. F. Bailey; F. O. Obe; A. P. Huntley, Will the Digital Mass Filter Be the Next High-Resolution High-Mass Analyzer? Journal of the American Society for Mass Spectrometry 2021, 32 (10), 2615-2620.

[3]  J. W. McCabe; B. J. Jones; T. E. Walker; R. L. Schrader; A. P. Huntley; J. Lyu; N. M. Hoffman; G. A. Anderson; P. T. Reilly; A. Laganowsky; V. H. Wysocki; D. H. Russell, Implementing Digital-Waveform Technology for Extended m/z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry 2021, 32 (12), 2812-2820.

[4]  A. P. Huntley; P. T. A. Reilly, Quantifying the operation of sinusoidal mass filters. J Mass Spectrom 2021, 56 (2), e4703.

[5]  A. P. Huntley; P. T. A. Reilly, Computational evaluation of a new digital tandem quadrupole mass filter. Journal of Mass Spectrometry 2021, 56 (2), e4699.

[6]  A. P. Huntley; P. T. A. Reilly, Computational evaluation of mass filter acceptance and transmittance influenced by developing fields: An application of the plane method to investigate prefilter efficacy for rectangular wave operated mass filters. J Mass Spectrom 2020, 55 (6), e4510.

[7]  A. P. Huntley; P. T. A. Reilly, New tools for theoretical comparison of rectangular and sine wave operation of ion traps, guides and mass filters. J Mass Spectrom 2020, 55 (12), e4661.

[8]  A. P. Huntley; G. F. Brabeck; P. T. A. Reilly, Influence of the RF drive potential on the acceptance behavior of pure quadrupole mass filters operated in stability zones A and B. International Journal of Mass Spectrometry 2020, 450, 116303.

[9]  M. E. Reece; A. P. Huntley; A. M. Moon; P. T. A. Reilly, Digital Mass Analysis in a Linear Ion Trap without Auxiliary Waveforms. Journal of the American Society for Mass Spectrometry 2019, 31 (1), 103-108.

[10]  A. P. Huntley; B. Opačić; G. F. Brabeck; P. T. Reilly, Simulation of instantaneous changes in ion motion with waveform duty cycle. International Journal of Mass Spectrometry 2019, 441, 8-13.

[11]  A. P. Huntley; G. F. Brabeck; P. T. A. Reilly, Tutorial and comprehensive computational study of acceptance and transmission of sinusoidal and digital ion guides. J Mass Spectrom 2019, 54 (11), 857-868.

[12]  B. Opačić; A. P. Huntley; B. H. Clowers; P. T. A. Reilly, Digital Mass Filter Analysis in Stability Zones A and B. Journal of Mass Spectrometry 2018, 53, 1155-1168.  .

[13]  B. Opačić; N. M. Hoffman; Z. P. Gotlib; B. H. Clowers; P. T. Reilly, Using digital waveforms to mitigate solvent clustering during mass filter analysis of proteins. Journal of The American Society for Mass Spectrometry 2018, 29 (10), 2081-2085.

[14]  B. Opačić; N. M. Hoffman; B. H. Clowers; P. T. A. Reilly, Impact of injection potential on measured ion response for digitally driven mass filters. International Journal of Mass Spectrometry 2018, 434, 1-6.

[15]  N. M. Hoffman; Z. P. Gotlib; B. Opačić; A. P. Huntley; A. M. Moon; K. E. Donahoe; G. F. Brabeck; P. T. Reilly, Digital waveform technology and the next generation of mass spectrometers. Journal of The American Society for Mass Spectrometry 2018, 29 (2), 331-341.

[16]  N. M. Hoffman; Z. P. Gotlib; B. Opačić; B. H. Clowers; P. T. Reilly, A comparison based digital waveform generator for high resolution duty cycle. Review of Scientific Instruments 2018, 89 (8), 084101.

[17]  N. M. Hoffman; B. Opačić; P. T. Reilly, Note: An inexpensive square waveform ion funnel driver. Review of Scientific Instruments 2017, 88 (1), 016104.

[18]  G. F. Brabeck; P. T. Reilly, Computational Analysis of Quadrupole Mass Filters Employing Nontraditional Waveforms. J Am Soc Mass Spectrom 2016, 27 (6), 1122-7.

[19]  G. F. Brabeck; H. Koizumi; E. Koizumi; P. T. Reilly, Characterization of quadrupole mass filters operated with frequency-asymmetric and amplitude-asymmetric waveforms. International Journal of Mass Spectrometry 2016, 404, 8-13.

[20]  P. T. A. Reilly; G. F. Brabeck, Mapping the pseudopotential well for all values of the Mathieu parameter q in digital and sinusoidal ion traps. International Journal of Mass Spectrometry 2015, 392, 86-90.

[21]  G. F. Brabeck; P. T. A. Reilly, Ion Manipulation by Digital Waveform Technology. Special Issues 2015, 13 (2), 34–44.

[22]  G. F. Brabeck; P. T. Reilly, Ion manipulation by digital waveform technology. In LCGC North America, 2015; pp 34-44.

[23]  G. F. Brabeck; P. T. A. Reilly, Mapping ion stability in digitally driven ion traps and guides. International Journal of Mass Spectrometry 2014, 364, 1-8.

[24]  G. F. Brabeck; H. Chen; N. M. Hoffman; L. Wang; P. T. A. Reilly, Development of MSn in Digitally Operated Linear Ion Guides. Analytical Chemistry 2014, 86 (15), 7757-7763.

[25]  R. Singh; V. Jayaram; P. T. A. Reilly, Duty cycle-based isolation in linear quadrupole ion traps. International Journal of Mass Spectrometry 2013, 343, 45-49.

[26]  G. F. Brabeck; V. Jayaram; R. Singh; P. T. A. Reilly In Duty Cycle-Based Cross Section Measurement of Large Singly-Charged Proteins, 61ST ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, MN, Minneapolis, MN, 2013.

[27]  X. Wang; H. Chen; J. Lee; P. T. A. Reilly, Increasing the trapping mass range to m/z=10(9)-A major step toward high resolution mass analysis of intact RNA, DNA and viruses. International Journal of Mass Spectrometry 2012, 328, 28-35.

[28]  K. Saito; P. T. A. Reilly; E. Koizumi; H. Koizumi, A hybrid approach to calculating Coulombic interactions: An effective and efficient method for optimization of simulations of many ions in quadrupole ion storage device with SIMION. International Journal of Mass Spectrometry 2012, 315, 74-80.

[29]  P. T. A. Reilly; H. Chen; X. Wang; K. G. E. Donahoe, High resolution TOF-MS of intact singly charged proteins and complexes up to m/z=1,000,000. Abstracts of Papers of the American Chemical Society 2012, 244.

[30]  T. Liu; J. R. Nedrow-Byers; M. R. Hopkins; L. Y. Wu; J. Lee; P. T. A. Reilly; C. E. Berkman, Targeting prostate cancer cells with a multivalent PSMA inhibitor-guided streptavidin conjugate. Bioorganic & Medicinal Chemistry Letters 2012, 22 (12), 3931-3934.

[31]  H. Chen; J. Lee; P. T. A. Reilly, High-resolution ultra-high mass spectrometry: Increasing the m/z range of protein analysis. Proteomics 2012, 12 (19-20), 3020-3029.

[32]  J. Lee; P. T. A. Reilly, Limitation of Time-of-Flight Resolution in the Ultra High Mass Range. Analytical Chemistry 2011, 83 (15), 5831-5833.

[33]  J. Lee; M. A. Marino; H. Koizumi; P. T. A. Reilly, Simulation of duty cycle-based trapping and ejection of massive ions using linear digital quadrupoles: The enabling technology for high resolution time-of-flight mass spectrometry in the ultra high mass range. International Journal of Mass Spectrometry 2011, 304 (1), 36-40.

[34]  J. Lee; H. Koizumi; P. T. A. Reilly In Duty Cycle Manipulation of Digital Quadrupoles—the Enabling Technology for High Resolution Time-of-Flight Mass Spectrometry at m/z > 20,000 The American Society for Mass Spectrometry Denver, Denver, 2011.

[35]  J. Lee; H. Chen; T. Liu; C. E. Berkman; P. T. A. Reilly, High Resolution Time-of-Flight Mass Analysis of the Entire Range of Intact Singly-Charged Proteins. Analytical Chemistry 2011, 83, 9406-9412.

[36]  H. Koizumi; W. B. Whitten; P. T. A. Reilly, Controlling the Expansion into Vacuum—the Enabling Technology for Trapping Atmosphere-Sampled Particulate Ions Journal of the American Society for Mass Spectrometry 2010, 21 (1), 242-248.

[37]  H. Koizumi; B. Jatko; W. H. Andrews; W. B. Whitten; P. T. A. Reilly, A novel phase-coherent programmable clock for high-precision arbitrary waveform generation applied to digital ion trap mass spectrometry. International Journal of Mass Spectrometry 2010, 292 (1-3), 23-31.