A Time-of-Flight Mass Spectrometer for Upper Atmospheric Measurements

The mesosphere-lower thermosphere (MLT) is perhaps the least understood region of the earth’s atmosphere due to the difficulty of obtaining in-situ measurements. Access to the MLT is limited to high-speed sounding rockets for brief periods of at most a few minutes. Because of its wide mass range and high scan rate, Time-of-flight mass spectrometry (TOF-MS) has potential to resolve thin layers of diverse species in the MLT. However, because ambient pressures can reach into the millitorr range, TOF-MS has rarely been applied in the MLT due to its dependence on high voltages and microchannel plate (MCP) detectors. A novel dual mode, compact axial TOF-MS suitable for deployment aboard a sounding rocket for measurements in the MLT is presented. This TOF-MS is capable of operating in either a standard TOF mode or in a multiplexing mode to achieve high measurement duty cycles with a theoretically unlimited mass range. Experimental data is presented demonstrating successful MCP operation in a variety of environments including O2, N2, and air at pressures into the low millitor range. Also presented are results from extensive simulation and modeling efforts to approximate the in-flight operating environment of the TOF-MS. Gas flow modeling in a typical MLT environment is performed using the Direct Simulation Monte Carlo (DSMC) method. Standard gas flow equations are combined with DSMC results to estimate pressures inside the TOF-MS. Modeling, simulations and experimental work combine to demonstrate the potential of the new dual mode TOF-MS for deployment in the upper atmosphere

An Axial Time-of-flight Mass Spectrometer for Upper Atmospheric Measurements

As the “shoreline” of the Earth’s atmosphere, the mesosphere/lower thermosphere (MLT) region is home to many interesting and important phenomena, the most visible of which are the auroras. Geomagnetic storms, in addition to causing very intense auroral activity, also deposit large amounts of energy into the earth’s ionosphere. Recent analysis of data from the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument aboard the Thermosphere-Ionosphere-Mesosphere Energetics and Dynamics (TIMED) satellite suggests that 5.3μm emission from vibrationally excited NO is the main method of energy dissipation from energy deposited by geomagnetic storms. Additionally, NO+ has been shown to be the major contributor to geomagnetic storm induced 4.3μm nighttime emission. In order to better physically understand these two large sources of geomagnetic storm energy dissipation, a sounding rocket mission, ROCKet-borne Storm Energetics of Auroral Dosing in the E-region (ROCK-STEADE) is being proposed. The ROCK-STEADE instrument suite consists of several photometers, an interferometer, an IR spectrometer, and two time-of-flight mass spectrometers (TOFMS). The TOFMS will measure the ion and neutral compositions in the atmosphere as the sounding rocket travels through the MLT. Due to the use of microchannel plate (MCP) detectors in TOFMS, one of the major challenges to making measurements in the MLT is the high ambient pressure. Other challenges and sources of error and background include stray UV photons, scattering of gas molecules from the interior surfaces of the instrument, dissociation of molecules in the bow shock caused by the supersonic rocket flight, and reactive recombination at the surfaces of the instrument. Methods of dealing with these challenges include: • Recent advances in MCP technology allowing MCP operation into the mtorr range • Cooling the front surface of the TOFMS using liquid He to eliminate the bow shock (thus making possible the direct sampling of the ambient atmosphere) • Cryogenically cooling the interior of the instrument to eliminate scattering of gas from instrument walls and therefore also reducing the contribution of reactive recombination • Rigorous error analysis to account for the background contribution of stray U

A New Mass Spectrometer for Upper Atmospheric Measurements in the Auroral Region

We have previously presented a new rocket-borne time-of-flight mass spectrometer (TOF-MS) for measurements in the mesosphere / lower thermosphere (MLT). Traditionally, mass spectrometry in the MLT has been difficult, mainly due to the elevated ambient pressures of the MLT and high speeds of a sounding rocket flight, which affect the direct sampling of the ambient atmosphere and spatial resolution. The TOF-MS is a versatile, inherently adaptable, axial-sampling instrument, capable of operating in a traditional TOF mode or in a multiplexing Hadamard-transform mode where high spatial resolution is desired. To minimize bow shock effects at low altitudes (~70-110km), the ram surface of the TOF-MS can be cryogenically cooled using liquid He to adsorb impinging gas particles. The vacuum pumping system for the TOF-MS is tailored to the specific mission and instrument configuration. Depending on the instrument gas load and operating altitude, cryo, miniature turbo pump or getter-based pumping systems may be employed. Terrestrial TOF-MS instruments often employ a reflectron, essentially an ion-mirror, to improve mass resolving power and compensate for the thermal velocity distribution of particles being measured. The TOF-MS can be arranged in either a simple linear or reflectron configuration. Simulations and modeling are used to compare instrument mass resolution for linear and reflectron configurations for several variable conditions including vehicle velocity and ambient temperature, ultimately demonstrating the potential to make rocket-borne mass spectrometry measurements with unit-mass resolution up to at least 48 amu. Preliminary analyses suggest that many species of interest (including He, CO2, O2, O2 , N2, N2 , and NO ) can be measured with an uncertainty below 10% relative standard deviation on a sounding rocket flight. We also present experimental data for a laboratory prototype linear TOF-MS. Experimental data is compared to simulation and modeling efforts to validate and confirm instrument performance and capability. Two proposed rocket campaigns for investigations of the auroral region include the TOF-MS. By making accurate composition measurements of the neutral atmosphere from 70 to 120km, Mass Spectrometry of the Turbopause Region (MSTR) aims to improve the accuracy of temperature measurements in the turbopause region, improve the MSIS model atmosphere and examine the transition from the turbulently mixed lower atmosphere to the diffusive equilibrium of the upper atmosphere. The ROCKet-borne STorm Energetics of Auroral Dosing in the E-region (ROCK-STEADE) mission will study energy transfer in the E-region during an aurora by examining auroral emissions and measuring concentrations of neutrals and ions. The instrument suite for ROCK-STEADE includes two mass spectrometers, one each to measure neutrals and ions in the altitude range of 70 - 170km. The ability of the TOF-MS instrument to make accurate measurements will greatly aid in better understanding the MLT

Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification.Here, we have investigated the electron capture dissociation (ECD) and collision-induced association (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains

Hydrogen Bonding Constrains Free Radical Reaction Dynamics at Serine and Threonine Residues in Peptides

Free radical-initiated peptide sequencing (FRIPS) mass spectrometry derives advantage from the introduction of highly selective low-energy dissociation pathways in target peptides. An acetyl radical, formed at the peptide N-terminus via collisional activation and subsequent dissociation of a covalently attached radical precursor, abstracts a hydrogen atom from diverse sites on the peptide, yielding sequence information through backbone cleavage as well as side-chain loss. Unique free-radical-initiated dissociation pathways observed at serine and threonine residues lead to cleavage of the neighboring N-terminal C_α–C or N–C_α bond rather than the typical Cα–C bond cleavage observed with other amino acids. These reactions were investigated by FRIPS of model peptides of the form AARAAAXAA, where X is the amino acid of interest. In combination with density functional theory (DFT) calculations, the experiments indicate the strong influence of hydrogen bonding at serine or threonine on the observed free radical chemistry. Hydrogen bonding of the side-chain hydroxyl group with a backbone carbonyl oxygen aligns the singly occupied π orbital on the β-carbon and the N–C_α bond, leading to low-barrier β-cleavage of the N–C_α bond. Interaction with the N-terminal carbonyl favors a hydrogen-atom transfer process to yield stable c and z• ions, whereas C-terminal interaction leads to effective cleavage of the C_α–C bond through rapid loss of isocyanic acid. Dissociation of the C_α–C bond may also occur via water loss followed by β-cleavage from a nitrogen-centered radical. These competitive dissociation pathways from a single residue illustrate the sensitivity of gas-phase free radical chemistry to subtle factors such as hydrogen bonding that affect the potential energy surface for these low-barrier processes