Technological developments in mass spectrometry towards molecular structural elucidation of macromolecular assemblies

Retrieving higher-order structural features of macromolecular assemblies (MMAs), such as protein complexes and viruses, is of great interest. These characteristics are crucial for understanding the functions and interactions of MMAs with other molecular species or receptors. While various techniques such as cryogenic-electron microscopy, nuclear magnetic resonance, and x-ray crystallography are capable of providing high-resolution structures of MMAs, they come with some limitations. This thesis primarily focuses on the technological developments in mass spectrometry (MS) in retrieving molecular features of MMAs at different levels of their organization. For that, aspects of soft-ionizing techniques (nano-electrospray ionization and matrix-assisted laser desorption/ionization), axial/orthogonal reflectron time-of-flight and high-resolution Orbitrap MS, top-down proteomics (ultraviolet photodissociation and higher-energy collisional dissociation), and mass-to-charge ratio/time-resolved imaging using pixelated Timepix and Timepix3 application-specific integrated circuit based detection assemblies were brought together

Infrared Laser Desorption and Electrospray Ionisation of Non‐Covalent Protein Complexes: Generation of Intact, Multiply Charged Species

We present a novel method enabling the infrared laser desorption and electrospray ionisation (ESI) of protein complexes in their native state. Using this method, we demonstrate the surprising generation of intact, multiply charged ions of myoglobin, non-covalent haemoglobin complex, and intact immunoglobulin G antibody in their native states. The observation of a surviving population of intact non-covalent complexes is characteristic of the low internal energy build-up experienced during both laser desorption from solution and subsequent ionisation. Compared to conventional nano-ESI, this approach yielded slightly lower average charge states suggesting additional maintenance of tertiary structure during desorption and ionisation, and is more tolerant to salts enabling simpler sample purification procedures. This approach may enable the development of high-throughput native-MS methods capable of analysing the composition and sequence of multiple macromolecular samples per minute

Study of the transient nature of classical Be stars using multi-epoch optical spectroscopy

Variability is a commonly observed property of classical Be stars (CBe) stars. In extreme cases, complete disappearance of the H{\alpha} emission line occurs, indicating a disc-less state in CBe stars. The disc-loss and reappearing phases can be identified by studying the H{\alpha} line profiles of CBe stars on a regular basis. In this paper, we present the study of a set of selected 9 bright CBe stars, in the wavelength range of 6200 - 6700 {\AA}, to better understand their disc transient nature through continuous monitoring of their H{\alpha} line profile variations for 5 consecutive years (2015 -- 2019). Based on our observations, we suggest that 4 of the program stars (HD 4180, HD 142926, HD 164447 and HD 171780) are possibly undergoing disc-loss episodes, whereas one other star (HD 23302) might be passing through disc formation phase. The remaining 4 stars (HD 237056, HD 33357, HD 38708 and HD 60855) have shown signs of hosting a stable disc in recent epochs. Through visual inspection of the overall variation observed in the H{\alpha} EW for these stars, we classified them into groups of growing, stable and dissipating discs, respectively. Moreover, our comparative analysis using the BeSS database points out that the star HD 60855 has passed through a disc-less episode in 2008, with its disc formation happening probably over a timescale of only 2 months, between January and March 2008.Comment: 19 pages, 7 figures, 2 tables, accepted in JAp

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio ( m/ z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase

Infrared Laser Desorption and Electrospray Ionisation of Non‐Covalent Protein Complexes: Generation of Intact, Multiply Charged Species

We present a novel method enabling the infrared laser desorption and electrospray ionisation (ESI) of protein complexes in their native state. Using this method, we demonstrate the surprising generation of intact, multiply charged ions of myoglobin, non-covalent haemoglobin complex, and intact immunoglobulin G antibody in their native states. The observation of a surviving population of intact non-covalent complexes is characteristic of the low internal energy build-up experienced during both laser desorption from solution and subsequent ionisation. Compared to conventional nano-ESI, this approach yielded slightly lower average charge states suggesting additional maintenance of tertiary structure during desorption and ionisation, and is more tolerant to salts enabling simpler sample purification procedures. This approach may enable the development of high-throughput native-MS methods capable of analysing the composition and sequence of multiple macromolecular samples per minute

Time-Resolved Imaging of High Mass Proteins and Metastable Fragments Using Matrix-Assisted Laser Desorption/Ionization, Axial Time-of-Flight Mass Spectrometry, and TPX3CAM

The Timepix (TPX) is a position- and time-sensitive pixelated charge detector that can be coupled with time-of-flight mass spectrometry (TOF MS) in combination with microchannel plates (MCPs) for the spatially and temporally resolved detection of biomolecules. Earlier generation TPX detectors used in previous studies were limited by a moderate time resolution (at best 10 ns) and single-stop detection for each pixel that hampered the detection of ions with high mass-to-charge (m/z) values at high pixel occupancies. In this study, we have coupled an MCP-phosphor screen-TPX3CAM detection assembly that contains a silicon-coated TPX3 chip to a matrix-assisted laser desorption/ionization (MALDI)-axial TOF MS. A time resolution of 1.5625 ns, per-pixel multihit functionality, simultaneous measurement of TOF and time-over-threshold (TOT) values, and kHz readout rates of the TPX3 extended the m/z detection range of the TPX detector family. The detection of singly charged intact Immunoglobulin M ions of m/z value approaching 1 × 106 Da has been demonstrated. We also discuss the utilization of additional information on impact coordinates and TOT provided by the TPX3 compared to conventional MS detectors for the enhancement of the quality of the mass spectrum in terms of signal-to-noise (S/N) ratio. We show how the reduced dead time and event-based readout in TPX3 compared to the TPX improves the sensitivity of high m/z detection in both low and high mass measurements (m/z range: 757-970,000 Da). We further exploit the imaging capabilities of the TPX3 detector for the spatial and temporal separation of neutral fragments generated by metastable decay at different locations along the field-free flight region by simultaneous application of deflection and retarding fields

Time-Resolved Imaging of High Mass Proteins and Metastable Fragments Using Matrix-Assisted Laser Desorption/Ionization, Axial Time-of-Flight Mass Spectrometry, and TPX3CAM

The Timepix (TPX) is a position- and time-sensitive pixelated charge detector that can be coupled with time-of-flight mass spectrometry (TOF MS) in combination with microchannel plates (MCPs) for the spatially and temporally resolved detection of biomolecules. Earlier generation TPX detectors used in previous studies were limited by a moderate time resolution (at best 10 ns) and single-stop detection for each pixel that hampered the detection of ions with high mass-to-charge (m/z) values at high pixel occupancies. In this study, we have coupled an MCP-phosphor screen-TPX3CAM detection assembly that contains a silicon-coated TPX3 chip to a matrix-assisted laser desorption/ionization (MALDI)-axial TOF MS. A time resolution of 1.5625 ns, per-pixel multihit functionality, simultaneous measurement of TOF and time-over-threshold (TOT) values, and kHz readout rates of the TPX3 extended the m/z detection range of the TPX detector family. The detection of singly charged intact Immunoglobulin M ions of m/z value approaching 1 × 106 Da has been demonstrated. We also discuss the utilization of additional information on impact coordinates and TOT provided by the TPX3 compared to conventional MS detectors for the enhancement of the quality of the mass spectrum in terms of signal-to-noise (S/N) ratio. We show how the reduced dead time and event-based readout in TPX3 compared to the TPX improves the sensitivity of high m/z detection in both low and high mass measurements (m/z range: 757-970,000 Da). We further exploit the imaging capabilities of the TPX3 detector for the spatial and temporal separation of neutral fragments generated by metastable decay at different locations along the field-free flight region by simultaneous application of deflection and retarding fields

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.</p

Ion Imaging of Native Protein Complexes Using Orthogonal Time-of-Flight Mass Spectrometry and a Timepix Detector

Native mass spectrometry (native MS) has emerged as a powerful technique to study the structure and stoichiometry of large protein complexes. Traditionally, native MS has been performed on modified time-of-flight (TOF) systems combined with detectors that do not provide information on the arrival coordinates of each ion at the detector. In this study, we describe the implementation of a Timepix (TPX) pixelated detector on a modified orthogonal TOF (O-TOF) mass spectrometer for the analysis and imaging of native protein complexes. In this unique experimental setup, we have used the impact positions of the ions at the detector to visualize the effects of various ion optical parameters on the flight path of ions. We also demonstrate the ability to unambiguously detect and image individual ion events, providing the first report of single-ion imaging of protein complexes in native MS. Furthermore, the simultaneous space- and time-sensitive nature of the TPX detector was critical in the identification of the origin of an unexpected TOF signal. A signal that could easily be mistaken as a fragment of the protein complex was explicitly identified as a secondary electron signal arising from ion-surface collisions inside the TOF housing. This work significantly extends the mass range previously detected with the TPX and exemplifies the value of simultaneous space- and time-resolved detection in the study of ion optical processes and ion trajectories in TOF mass spectrometers

Ion Imaging of Native Protein Complexes Using Orthogonal Time-of-Flight Mass Spectrometry and a Timepix Detector

Native mass spectrometry (native MS) has emerged as a powerful technique to study the structure and stoichiometry of large protein complexes. Traditionally, native MS has been performed on modified time-of-flight (TOF) systems combined with detectors that do not provide information on the arrival coordinates of each ion at the detector. In this study, we describe the implementation of a Timepix (TPX) pixelated detector on a modified orthogonal TOF (O-TOF) mass spectrometer for the analysis and imaging of native protein complexes. In this unique experimental setup, we have used the impact positions of the ions at the detector to visualize the effects of various ion optical parameters on the flight path of ions. We also demonstrate the ability to unambiguously detect and image individual ion events, providing the first report of single-ion imaging of protein complexes in native MS. Furthermore, the simultaneous space- and time-sensitive nature of the TPX detector was critical in the identification of the origin of an unexpected TOF signal. A signal that could easily be mistaken as a fragment of the protein complex was explicitly identified as a secondary electron signal arising from ion-surface collisions inside the TOF housing. This work significantly extends the mass range previously detected with the TPX and exemplifies the value of simultaneous space- and time-resolved detection in the study of ion optical processes and ion trajectories in TOF mass spectrometers