In Situ Metallic Coating of Atom Probe Specimen for Enhanced Yield, Performance, and Increased Field-of-View

Atom probe tomography requires needle-shaped specimens with a diameter typically below 100 nm, making them both very fragile and reactive, and defects (notches at grain boundaries or precipitates) are known to affect the yield and data quality. The use of a conformal coating directly on the sharpened specimen has been proposed to increase yield and reduce background. However, to date, these coatings have been applied ex situ and mostly are not uniform. Here, we report on the controlled focused-ion beam in situ deposition of a thin metal film on specimens immediately after specimen preparation. Different metallic targets e.g. Cr were attached to a micromanipulator via a conventional lift-out method and sputtered using Ga or Xe ions. We showcase the many advantages of coating specimens from metallic to nonmetallic materials. We have identified an increase in data quality and yield, an improvement of the mass resolution, as well as an increase in the effective field-of-view. This wider field-of-view enables visualization of the entire original specimen, allowing to detect the complete surface oxide layer around the specimen. The ease of implementation of the approach makes it very attractive for generalizing its use across a very wide range of atom probe analyses.

Testing the Influence of Laser Pulse Energy and Rate in the Atom Probe Tomography Analysis of Minerals

The use of atom probe tomography (APT) for mineral analysis is contributing to fundamental studies in Earth Sciences. Meanwhile, the need for standardization of this technique is becoming evident. Pending the use of mineral standards, the optimization of analysis parameters is needed to facilitate the study of different mineral groups in terms of data collection and quality. The laser pulse rate and energy are variables that highly affect the atom evaporation process occurring during APT analysis, and their testing is important to forecast mineral behavior and obtain the best possible data. In this study, five minerals representative of major groups (albite, As-pyrite, barite, olivine, and monazite) were analyzed over a range of laser pulse energies (10-50 pJ) and rates (100-250 kHz) to assess output parameter quality and evaluate compositional estimate stoichiometry. Among the studied minerals, As-pyrite, with the higher thermal conductivity and lower band gap, was the most affected by the laser pulse variation. Chemical composition estimates equal or close to the general chemical formula were achieved for monazite and As-pyrite. The analysis of multihit events has proved to be the best strategy to verify the efficacy of the evaporation process and to evaluate the best laser pulse setting for minerals.

Tailoring the Sensitivity of Microcantilevers To Monitor the Mass of Single Adherent Living Cells

Microcantilevers are widely employed as mass sensors for biological samples, from single molecules to single cells. However, the accurate mass quantification of living adherent cells is impaired by the microcantilever's mass sensitivity and cell migration, both of which can lead to detect masses mismatching by ≫50%. Here, we design photothermally actuated microcantilevers to optimize the accuracy of cell mass measurements. By reducing the inertial mass of the microcantilever using a focused ion beam, we considerably increase its mass sensitivity, which is validated by finite element analysis and experimentally by gelatin microbeads. The improved microcantilevers allow us to instantly monitor at much improved accuracy the mass of both living HeLa cells and mouse fibroblasts adhering to different substrates. Finally, we show that the improved cantilever design favorably restricts cell migration and thus reduces the large measurement errors associated with this effect.

Simulation of a Miniature Linear Ion Trap with Half-Round Rod Electrodes

The miniaturization of ion trap mass analyzers is an important direction in the development of mass spectrometers. In this work, we proposed two models of miniaturized HreLIT with a field radius of about 2 mm based on the existing research on conventional HreLIT and other ion traps, one with ions ejection slits on one pair of electrodes only (2-slit model) and the other with the same slits on all electrodes (4-slit model). The relationship of mass resolution with r/r_x and the "stretch" distance of electrodes in the ejection direction is investigated by theoretical simulations. Trends of electric fields inside the ion traps were discussed as well. The comparable maximum resolution is observed at r/r_x = 2/1.4 in both models, but stretching simulations revealed that the peak resolution of the 2-slit model was higher than that of the other model by about 8%. The highest value of 517 was obtained when stretching 1.1 mm. Furthermore, the resolution of ions with m/z = 119 could exceed 1000 when the scan rate was reduced to 800 Th/s. The mass spectrometry capability of miniature HreLIT has been confirmed theoretically, and it laid the foundation for the subsequent fabrication with MEMS technology.

Simulation of the simultaneous dual-frequency resonance excitation of ions in a linear ion trap

The process of ion resonance dipolar excitation in a linear ion trap by 2 ejection waveforms with close frequencies is studied. The physical mechanism of increasing the resolving power using the ion excitation is a nonlinearity of the electric radio frequency fields caused by space charge. Using 2 resonance forces with 2 close frequencies leads to the completion of 2 excitation processes. In the case of the perfect quadrupole electric field, the ion motion equations are linear, and as a result, the respondent ion ensemble is also a linear and valid superposition principle. Nevertheless, the resolution increases (20%) in the case of lack of a space charge in an operating mode with a dual-frequency. The numerical simulations show that the mass shift is removed, and the mass resolution is increased via dual-frequency resonance excitation when the frequency difference (approximately 2.5 kHz) is relatively small and the phase difference of 2 harmonic signals is 0-π3 even at a high linear ion density of up to 50 000 ions per radius field r₀ .

Optimizing Atom Probe Analysis with Synchronous Laser Pulsing and Voltage Pulsing

Atom probe has been developed for investigating materials at the atomic scale and in three dimensions by using either high-voltage (HV) pulses or laser pulses to trigger the field evaporation of surface atoms. In this paper, we propose an atom probe setup with pulsed evaporation achieved by simultaneous application of both methods. This provides a simple way to improve mass resolution without degrading the intrinsic spatial resolution of the instrument. The basic principle of this setup is the combination of both modes, but with a precise control of the delay (at a femtosecond timescale) between voltage and laser pulses. A home-made voltage pulse generator and an air-to-vacuum transmission system are discussed. The shape of the HV pulse presented at the sample apex is experimentally measured. Optimizing the delay between the voltage and the laser pulse improves the mass spectrum quality.

Understanding the characteristics of mass spectrometry data through the use of simulation

BACKGROUND

Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids. The potential importance of these clinical applications has made the development of better methods for processing and analyzing the data an active area of research. It is, however, difficult to determine which methods are better without knowing the true biochemical composition of the samples used in the experiments.

METHODS

We developed a mathematical model based on the physics of a simple MALDI-TOF mass spectrometer with time-lag focusing. Using this model, we implemented a statistical simulation of mass spectra. We used the simulation to explore some of the basicoperating characteristics of MALDI or SELDI instruments.

RESULTS

The simulation reproduced several characteristics of actual instruments. We found that the relative mass error is affected by the time discretization of the detector (about 0.01%) and the spread of initial velocities (about 0.1%). The accuracy of calibration based on external standards decays rapidly outside the range spanned by the calibrants. Natural isotope distributions play a major role inbroadening peaks associated with individual proteins. The area of a peak is a more accurate measure of its size than the height.

CONCLUSIONS

The model described here is capable of simulating realistic mass spectra. The simulation should become a useful tool forgenerating spectra where the true inputs are known, allowing researchers to evaluate the performance of new methods for processing and analyzing mass spectra.

AVAILABILITY

http://bioinformatics.mdanderson.org/cromwell.html.