Visualisation in imaging mass spectrometry using the minimum noise fraction transform

Extent: 6p.Background: Imaging Mass Spectrometry (IMS) provides a means to measure the spatial distribution of biochemical features on the surface of a sectioned tissue sample. IMS datasets are typically huge and visualisation and subsequent analysis can be challenging. Principal component analysis (PCA) is one popular data reduction technique that has been used and we propose another; the minimum noise fraction (MNF) transform which is popular in remote sensing. Findings: The MNF transform is able to extract spatially coherent information from IMS data. The MNF transform is implemented through an R-package which is available together with example data from http://staff.scm.uws.edu.au/∼glenn/#Software. Conclusions: In our example, the MNF transform was able to find additional images of interest. The extracted information forms a useful basis for subsequent analyses.Glenn Stone, David Clifford, Johan OR Gustafsson, Shaun R McColl and Peter Hoffman

In-situ, real-time, studies of film growth processes using ion scattering and direct recoil spectroscopy techniques.

Time-of-flight ion scattering and recoil spectroscopy (TOF-ISARS) enables the characterization of the composition and structure of surfaces with 1-2 monolayer specificity. It will be shown that surface analysis is possible at ambient pressures greater than 3 mTorr using TOF-ISARS techniques; allowing for real-time, in situ studies of film growth processes. TOF-ISARS comprises three analytical techniques: ion scattering spectroscopy (ISS), which detects the backscattered primary ion beam; direct recoil spectroscopy (DRS), which detects the surface species recoiled into the forward scattering direction; and mass spectroscopy of recoiled ions (MSRI), which is 3 variant of DRS capable of isotopic resolution for all surface species--including H and He. The advantages and limitations of each of these techniques will be discussed. The use of the three TOF-ISARS methods for real-time, in situ film growth studies at high ambient pressures will be illustrated. It will be shown that MSRI analysis is possible during sputter deposition. It will be also be demonstrated that the analyzer used for MSRI can also be used for time of flight secondary ion mass spectroscopy (TOF-SIMS) under high vacuum conditions. The use of a single analyzer to perform the complimentary surface analytical techniques of MSRI and SIMS is unique. The dwd functionality of the MSRI analyzer provides surface information not obtained when either MSRI or SIMS is used independently

The use of reactive ion sputtering to produce clean germanium surfaces in a carbon rich environment -- An ion scattering study

The authors have used the ion spectroscopic techniques of direct recoil spectroscopy (DRS) and mass spectroscopy of recoiled ions (MSRI) to demonstrate that low energy reactive ion sputtering of Ge is capable of removing surface impurities such as carbon. The experiments were performed in a vacuum chamber maintained at 3.5 {times} 10{sup {minus}7} Torr. At these pressures, physical sputtering using noble gas is not effective for cleaning Ge surfaces as carbon re-deposits onto the surface. In this paper, the authors demonstrate that reactive sputtering of Ge using 4.0 keV nitrogen at a Ge surface temperature of {approximately} 740 K and above removes surface carbon and deposits nitrogen on the Ge surface. Heating the nitrogen exposed Ge surface to above {approximately} 880 K results in the desorption of nitrogen and generates an atomically clean Ge surface, under poor vacuum conditions

Surface analysis of all elements with isotopic resolution at high ambient pressures using ion spectroscopic techniques

The authors have developed a mass spectrometer capable of surface analysis using the techniques of secondary ion mass spectroscopy (SIMS) and mass spectroscopy of recoiled ions (MSRI). For SIMS, an energetic ion beam creates a collision cascade which results in the ejection of low kinetic energy secondary ions from the surface being analyzed. The low kinetic energy SIMS ions are very susceptible to charge neutralization with the surface, and as a result, the SIMS ion yield varies by orders of magnitude depending on the chemical state of the surface. SIM spectra contain elemental ions, and molecular ions. For MSRI, a pulsed ion beam induces a binary collision with the surface being analyzed and the surface species are recoiled into the forward scattering direction with a large kinetic energy. The violence of the binary collision results in complete molecular decomposition, and only elemental ions are detected. The high kinetic energy MSRI ions are much less susceptible to charge neutralization with the surface than the low kinetic energy SIMS ions. In MSRI, the ion yield typically varies by less than a factor of ten as the chemical state of the surface changes--simplifying quantitative analysis vs. SIMS. In this paper, they authors will demonstrate that the high kinetic energy MSRI ions are able to transverse high pressure paths with only a reduction in peak intensity--making MSRI an ideal tool for real-time, in-situ film growth studies. The use of a single analyzer for both MSRI and SIMS is unique and provides complimentary information