Kenneth P. Garrard

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

AbstractDuring the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

Tool force and deflection compensation for small milling tools

A technique to compensate for deflection of small milling tools (diameter < 1 mm) has been demonstrated. This open-loop technique involves predicting the cutting and thrust forces, applying these forces to the tool, calculating the shape error due to tool deflection and creating a new tool path to eliminate this error. The tool force model has evolved from a decade of research to predict the forces in diamond turning. This model was modified to include the effects of tool rotation in milling as well as the changes in contact area and force direction using a ball end mill to create a free form surface. Experimental measurements were made to corroborate the components of the tool forces in the cutting and thrust directions. The force model was then combined with tool stiffness to calculate the deflection of the tool as a function of the depth of cut, the up-feed per revolution and the geometry of the part. Two experiments were used to demonstrate the effectiveness of this error compensation technique-a slot and a large circular groove. Each experiment reduced the error due to tool deflection by an order of magnitude from 20-50 μm to 2-5 μm.

A controller architecture for integrating a fast tool servo into a diamond turning machine

Abstract Diamond turning has become an important fabrication technique for producing reflective optics. However, the generation of a general optical surface requires the capability to fabricate nonrotationally symmetric surfaces. Current commercial diamond turning machines cannot perform this task at production rates because of the limited bandwidth of their axis motions and the limited update speed of their controllers. Although a fast tool servo overcomes the bandwidth limitation, the problem of integrating a fast control process (for the servo axis) and a slower control process (for the slide axes) remains. This article describes the computer hardware and software required to integrate a high-speed, low-amplitude fast tool servo into a conventional T-based diamond turning machine. This system can machine θ-dependent features, synchronized to the radial and axial position of the tool, up to the displacement of range of the servo. A set of interface boards have been designed and built that pass the position feedback data from the laser interferometer to both a high-speed servo controller and a slower slide axes controller. This design allows the fast tool servo to be an independent add-on accessory to the diamond turning machine and successfully incorporates nonrotationally symmetric fabrication capability. As an example of the surfaces possible with this system, an off-axis segment of a parabolic mirror has been machined on-axis. The peak-to-valley figure error of this 125-mm optic is less than 1.1 waves (0.7 μm).

Design tools for freeform optics

Freeform Optical surfaces are defined as any non-rotationally symmetric surface or a symmetric surface that is rotated about any axis that is not its axis of symmetry. These surfaces offer added degrees of freedom that can lead to lower wavefront error and smaller system size as compared to rotationally symmetric surfaces. Unfortunately, freeform optics are viewed by many designers as more difficult and expensive to manufacture than rotationally symmetric optical surfaces. For some freeform surfaces this is true, but a designer has little or no feedback to quantify the degree of difficulty for manufacturing a surface. This paper describes a joint effort by Optical Research Associates (ORA) and the Precision Engineering Center (PEC) at North Carolina State University to integrate metrics related to the cost and difficulty of manufacturing a surface into the merit function that is used during the design of an optical system using Code V. By incorporating such information into the merit function, it is possible to balance optical performance and manufacturability early in the design process.

Design and fabrication of diamond-machined aspheric mirrors for ground-based near-IR astronomy

Challenges in fabrication and testing have historically limited the choice of surfaces available for the design of reflective optical instruments. Spherical and conic mirrors are common, but, for future science instruments, more degrees of freedom will be necessary to meet performance and packaging requirements. These instruments will be composed of surfaces of revolution located far off-axis with large spherical departure, and some designs will even require asymmetric surface profiles. We describe the design and diamond machining of seven aluminum mirrors: three rotationally symmetric, off-axis conic sections, one off-axis biconic, and three flat mirror designs. These mirrors are for the Infrared Multi-Object Spectrometer instrument, a facility instrument for the Kitt Peak National Observatory’s Mayall Telescope (3.8 m) and a pathfinder for the future Next Generation Space Telescope multi-object spectrograph. The symmetric mirrors include convex and concave prolate and oblate ellipsoids, and range in aperture from 92 x 77 mm to 284 x 264 mm and in f-number from 0.9 to 2.4. The biconic mirror is concave and has a 94 x 76 mm aperture, (formula available in paper) and is decentered by -2 mm in x and 227 mm in y. The mirrors have an aspect ratio of approximately 6:1. The fabrication tolerances for surface error are < 63.3 nm RMS figure error and < 10 nm RMS microroughness. The mirrors are attached to the instrument bench using semi-kinematic, integral flexure mounts and optomechanically aligned to the instrument coordinate system using fiducial marks and datum surfaces. We also describe in-process profilometry and optical testing.

Silver dopants for targeted and untargeted direct analysis of unsaturated lipids via infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI).

RATIONALE Unsaturated lipids play a crucial role in cellular processes as signaling factors, membrane building blocks or energy storage molecules. However, adequate mass spectrometry imaging of this diverse group of molecules remains challenging. In this study we implemented silver cationization for direct analysis by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) to enhance the ion abundances for olefinic lipids and facilitate peak assignment. METHODS Trace amounts of silver nitrate were doped into the electrospray solvent of an IR-MALDESI imaging source coupled to an Orbitrap mass analyzer. Calcifediol was examined as a model compound to demonstrate the effect of silver dopants on sensitivity and assay robustness. Dried human serum spots were subsequently analyzed to compare Ag-doped solvents with previously described solvent compositions. Mass differences as well as ion abundance ratio filters were employed to interpret results based on the characteristic isotopic pattern of silver. RESULTS Olefinic lipids were readily observed as silver adducts in IR-MALDESI analyses. Silver cationization decreased the limit of detection for calcifediol by at least one order of magnitude and was not affected in complex biological matrices. The ion abundance ratio and mass difference of [M + (107) Ag(+)](+) and [M + (109) Ag(+)](+) were successfully applied to facilitate the spectral assignment of silver adducts. Overall, silver cationization increased the analyte coverage in human serum by 43% compared with a standard IR-MALDESI approach. CONCLUSIONS Silver cationization has been shown to enhance IR-MALDESI sensitivity and selectivity for unsaturated lipids, even when applied to complex samples. Increased compound coverage, enhanced robustness as well as the developed tools for peak assignment and mapping of isotopic patterns will clearly benefit future mass spectrometry imaging studies.

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

AbstractA major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstractᅟ

A high performance embedded machine tool controller

Abstract A Diamond Turning Machine (DTM) can fabricate components with extremely high precision and high quality surface finish characteristics. Existing commercial controllers are limited in their ability to support high performance machining and related advanced control algorithms. Evolving enhancements to the functional capability and control algorithms of a DTM require increased performance and flexibility from the computer system controlling it. To provide this capability the Precision Engineering Center at North Carolina State University has developed and implemented a high performance control system for such a machine tool. The control system is based on a heterogeneous hierarchical multiprocessor computer architecture. This provides the capacity to apply advanced control concepts to the DTM, resulting in improved precision and quality of machined parts. Additionally, the ability to machine non-rotationally symmetric components has been made possible by application of multiprocessor capability.

Characterization of the Spectral Accuracy of an Orbitrap Mass Analyzer Using Isotope Ratio Mass Spectrometry

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source coupled to the Q Exactive Plus has been extensively used in untargeted mass spectrometry imaging (MSI) analyses of biological tissue sections. Although the Orbitrap is a high-resolution and accurate-mass (HRAM) mass analyzer, these attributes alone cannot be used for the reliable identification of unknown analytes observed in complex biological matrices. Spectral accuracy (SA) is the ability of the mass spectrometer to accurately measure the isotopic distributions which, when used with high mass measurement accuracy (MMA), can facilitate the elucidation of a single elemental composition. To investigate the effects of different ion populations on an Orbitraps SA and MMA, a solution of caffeine, the tetrapeptide MRFA, and ultramark was analyzed using a Q Exactive Plus across eight distinct automatic gain control (AGC) targets. The same compounds from the same lot numbers were also individually analyzed using isotope ratio mass spectrometry (IRMS) to accurately determine the isotopic abundance of 13C, 15N, and 34S. We demonstrated that at optimum absolute ion abundances the Orbitrap can be used to accurately count carbons, nitrogens, and sulfurs in samples with varying masses. Additionally, absolute monoisotopic ion abundances required for high SA were empirically determined by using the expected (IRMS) and experimental (Orbitrap) isotopic distributions to calculate the Pearson chi-square test. These thresholds for absolute ion abundances can be used in untargeted MSI studies to shorten an identification list by rapidly screening for isotopic distributions whose absolute ion abundances are high enough to accurately estimate the number of atoms.

Automated Part Centering With Impulse Actuation

Centering a part on a spindle for precision machining is a tedious, time-consuming task. Currently, a skilled operator must measure the run-out of a part using a displacement gauge, then tap the part into place using a plastic or rubber hammer. This paper describes a method to automatically center a part on a vacuum chuck with initial run-out as large as 2.5 mm. The method involves measuring the magnitude and direction of the radial run-out and then actuating the part until the part and spindle centerlines are within 5 μm of each other. The run-out can be measured with either a touch probe mounted to a machine axis or an electronic gauge. The part is tapped into place with a linear actuator driven by a voice coil motor This paper includes an analysis of run-out measurement uncertainty as well as the design, performance modeling, and testing of the alignment actuator. This actuator was employed for part realignment and successfully positioned a hemispherical part with an initial run-out of 1-2.5 mm to within 5 μm of the spindle centerline. This capability shows that the run-out of a part manually placed on flat vacuum chuck can be automatically corrected.