Engineering topics
Wilson, Jesse W.
Publications and source records attributed to Wilson, Jesse W..
Top-down mass spectrometry of native proteoforms and their complexes: a community study
The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. Further, to address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.
Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins
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Influence of ion-pairing reagents on the separation of intact glycoproteins using hydrophilic-interaction liquid chromatography - high-resolution mass spectrometry
Hydrophilic-interaction liquid chromatography (HILIC) of intact proteins offers high-resolution separations of glycoforms of glycoproteins differing in the number of (neutral) glycans. However, to obtain efficient separations it is essential that the positively charged sites of the proteins are shielded by acidic (negative) ion-pair reagents (IPRs), so as to enhance the contribution of the hydroxyl groups of the (neutral) sugars in the glycoprotein. Here, we studied the influence of various IPRs that differ in physico-chemical properties, such as hydrophobicity and acidity, on the capillary-scale HILIC separation of intact (glyco)proteins. We evaluated the use of fluoroacetic acid (MFA), difluoroacetic acid (DFA), trifluoroacetic acid (TFA), and heptafluorobutyric acid (HFBA) as diluents for sample preparation, as solvents for sample loading on a reversed-phase trap prior to the HILIC separation, and as mobile-phase components for HILIC and HILIC-MS. To reduce the contribution of ion-exchange interaction with the (silica-based) stationary phase, we used an acrylamide-based monolithic column. We studied the influence of the different IPRs on each step of the separation of a mixture of proteins of different size and hydrophilicity and on the separation of the five glycoforms of ribonuclease B. The content of IPR in the sample was shown not to affect the separation and the MS detection. However, a low content of TFA and DFA in the mobile phase is favourable, as it reduces adduct formation and leads to higher signal intensity. The optimized HILIC conditions successfully resolved nine major glycoforms groups of a ~40 kDa glycoprotein horseradish peroxidase (HRP), as an example of a complex glycoprotein.
Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry
Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.
Nearly degenerate two-color impulsive coherent Raman hyperspectral imaging
Impulsive stimulated Raman scattering (ISRS) is a robust technique for studying low frequency (<300 cm –1 ) Raman vibrational modes, but ISRS has faced difficulty in translation to an imaging modality. A primary challenge is the separation of the pump and probe pulses. Here we introduce and demonstrate a simple strategy for ISRS spectroscopy and hyperspectral imaging that uses complementary steep edge spectral filters to separate the probe beam detection from the pump and enables simple ISRS microscopy with a single-color ultrafast laser source. ISRS spectra are obtained that span from the fingerprint region down to <50 cm –1 vibrational modes. Furthermore, hyperspectral imaging and polarization-dependent Raman spectra are also demonstrated.
High-throughput native mass spectrometry as experimental validation for in silico drug design
In this project, we developed automated workflows for both experimental validation and computational prediction of protein-ligand interactions. The ultimate goal is to establish an integrated pipeline for high throughput design of inhibitors to enzymes relevant to all areas of biological research. Our experimental approach is based on native mass spectrometry (native MS), which measures accurate masses and quantify the relative abundance of protein-ligand complexes to define binding affinity. We set up an in-house built autosampler with highly flexible configurations to minimize the manual steps for high throughput native MS. In parallel, we also performed manual native MS to characterize the binding of substrates and inhibitors of SARS-Cov-2 nonstructural protein nsp10/16 in order to optimize the experimental parameters for future automation. On the computational side, we streamlined the pipeline to achieve minimal manual intervention for predicting enzyme inhibitors via simulation, using the same nsp10/16 system as an example. Using the native MS method we examined 8 top-ranked designed compounds, 2 of which showed weak binding of ~50 µM. The information from native MS experiment provided critical insights and the foundation for a fully integrated workflow for enzyme inhibitor design.
Discovery of unknown posttranslational modifications by top-down mass spectrometry
Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).
High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity
SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1–20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer’s therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.
Phase noise limited frequency shift impulsive Raman spectroscopy
We introduce a method to enable optical amplification of a coherent Raman spectroscopy signal, which we call radio frequency (RF) Doppler Raman spectroscopy. In this article, we consider the perturbation of a probe pulse in a sample due to an excited Raman vibrational coherence as a generalized Doppler shift, which connects a time-varying optical path length (the product of the propagation length and refractive index, OPL = n ℓ) with an optical frequency shift. Amplification of a Raman signal outside of the focused interaction is enabled by converting the Doppler frequency shift experienced by a laser probe pulse into a periodic timing jitter. This transit time perturbation is detected through the phase of a RF electronic signal measured at a harmonic of the probe pulse train with a method adapted from precision metrology techniques used to measure laser pulse train timing jitter. Measurement of a timing jitter allows access to much lower noise floors than other coherent Raman techniques, and by exploiting the new capability to scale the signal of a coherent Raman spectroscopic signal, this method opens the potential to detect very weak Raman signals that are currently not observable due to limits of illumination intensity imposed by laser damage to the specimen and noise.
DR-RINS: Digital real-time relative intensity noise suppressor for pump–probe spectroscopy and microscopy
Relative intensity noise (RIN) inherent in fiber lasers poses a serious obstacle to their use in pump–probe spectroscopy and imaging. RIN can be removed through an analog balanced detector, or, as we have previously shown, software adaptive noise cancellation (ANC) on digitized signals. One major drawback to software ANC is the added time required for digitizing and post-processing. In this article, we describe a design for ANC on a field-programmable gate array (FPGA), making use of high-level synthesis tools and fixed-point arithmetic to achieve real-time laser RIN suppression at 25 MHz sample rates. Unlike the software-ANC approach, the FPGA-ANC device can serve as a dedicated drop-in denoiser, placed between the detectors and a commercial lock-in amplifier. We demonstrate its application to transient absorption spectroscopy and microscopy, lowering the noise floor to ~17 dB above the shot noise limit. Furthermore, we demonstrate a dramatic improvement in data acquisition time from ~6 h to ~5 min in a real-time imaging scenario.
Adaptive noise canceling for transient absorption microscopy
Significance: Ultrafast fiber lasers are an attractive alternative to bulk lasers for nonlinear optical microscopy for their compactness and low cost. The high relative intensity noise (RIN) of these lasers poses a challenge for pump-probe measurements such as transient absorption and stimulated Raman scattering, along with modalities that provide label-free contrast from the vibrational and electronic structure of molecules. Aim: Digital adaptive filtering was applied to determine the applicability for canceling laser RIN in a transient absorption microscope with an ultrafast fiber laser source. Approach: Digitized signals from the transmitted probe and reference photodetectors were fed to an adaptive filter in MATLAB, running in a noise canceling configuration. This result was then fed to a software lock-in algorithm to demodulate the pump-probe signal. Images were built up one line scan at a time with a 3.5-kHz resonant scanner, with 100× averaging. The imaging target was Bi4Ge3O12, which exhibits nondegenerate two-photon absorption at the pump/probe wavelengths used (530-nm pump and 490-nm probe). Results: Without adaptive noise cancellation, the lock-in output primarily passes the laser RIN within its detection bandwidth, resulting in images that closely follow the linear transmissivity and lack sensitivity to pump-probe time delay. With adaptive noise cancellation in front of the lock-in, the RIN rejection is enough to restore the z-sectioning and sensitivity to pump-probe delay, as expected for transient absorption. Results were limited primarily by noise from the photodetector and analog-to-digital converter. Conclusions: Digital adaptive noise cancellation, even when limited by electronics noise, can recover pump-probe signals by removal of laser RIN, under conditions where averaging alone fails.