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The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.
A tool for merging and/or rebinning single or multiple datasets to achieve a lower point density with best possible statistics. highly scriptable, CLI, no GUI
Version 0.1: works but could do with a cleanup. Weighting by uncertainty currently always on, but should be optional for use as an azimuthal or radial averager
IsoCor
(2022)
Despite numerous advantages offered by hyphenation of chromatography and electrokinetic separation methods with multicollector (MC) ICP-MS for isotope analysis, the main limitation of such systems is the decrease in precision and increase in uncertainty due to generation of short transient signals. To minimize this limitation, most authors compare several isotope ratio calculation methods and establish a multi-step data processing routine based on the precision and accuracy of the methods. However, to the best of our knowledge, there is no universal data processing tool available that incorporates all important steps of the treatment of the transient signals. Thus, we introduce a data processing application (App) IsoCor that facilitates automatic calculation of isotope ratios from transient signals and eases selection of the most suitable method. The IsoCor App performs baseline subtraction, peak detection, mass bias correction, isotope ratio calculation and delta calculation. The feasibility and reliability of the App was proven by reproducing the results from isotope analysis of three elements (neodymium, mercury and sulfur) measured on-line via hyphenated systems. The IsoCor App provides trackability of the results to ensure quality control of the analysis.
ABID
(2022)
In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
Wide-range X-ray scattering datasets and analyses for all samples described in the 2020 publication "Gold and silver dichroic nanocomposite in the quest for 3D printing the Lycurgus cup". These datasets are composed by combining multiple small-angle x-ray scattering and wide-angle x-ray scattering curves into a single dataset. They have been analyzed using McSAS to extract polydispersities and volume fractions. They have been collected using the MOUSE project (instrument and methodology).
Models for TOPAS/Geant4 to estimate the microscopic dose received by biomolecules during bioSAXS experiments.
The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org).
This sequence of X-Ray images shows how one of the most common Italian moka pots actually work! The sequence starts with a completely prepared moka pot (water in the bottom part, coffee in the middle and hot plate on). During the process the water starts to boil and the steam pressure pushes the hot water through the coffee into the bassin at the top of the pot.
This video sequence and additional explanations can also be found on Wikipedia.
X-Ray computed tomography (XCT) scan of 11 individual metallic powder particles, made of (Mn,Fe)2(P,Si) alloy. The data set consists of 4 single XCT scans which have been stitched together [3] after reconstruction. The powder material is an (Mn,Fe)2(P,Si) alloy with an average density of 6.4 g/cm³. The particle size range is about 100 - 150 µm with equivalent pore diameters up to 75 µm. The powder and the metallic alloy are described in detail in [1, 2].
This dataset contains raw data resulting from Impact-Echo measurements at the reference concrete block "IE Platte", located at BAM (German Federal Institute for Materials Research and Testing).
The specimen contains three polystyrene slabs and one polyethylene foil to act as reflectors. The specimen was produced in a three-step process. First, the base plate was cast. Second, the reflectors were taped to the base plate. Finally, the upper layer was cast on top of base plate and reflectors. A drawing is contained in the dataset.
The Impact-Echo method is based on the excitation of the zero-group-velocity frequency of the first symmetric Lamb mode of a plate-like structure, in order to assess its thickness. Numerous publications elaborate on Impact-Echo theory, examples are (Gibson and Popovics 2005, Schubert and Köhler 2008 , Abraham and Popovics 2010).
The measurements have been conducted using a setup that contains only commercially available components. The setup consists of an Olson CTG-2 concrete thickness gauge (Olsen Instruments, USA) for actuation and sensing and an 8-bit NI USB-5132 digital storage oscilloscope (National Instruments, USA) combined with the Echolyst software (Schweizerischer Verein für technische Inspektionen (SVTI), Switzerland) for data acquisition.
Measurements were conducted using a grid of 29x29 points with a spacing of 50 mm. At each point 8192 samples were recorded at a sampling rate of 1 MS/s.
The dataset contains the (X,Y) location in mm of the individual measurement points as well as the raw measurement data at those points.
The data is provided in the formats *.mir/*.mhdr (Echolyst), *.npy (Python) and *.mat (Matlab) and *.csv to ease the import in various post-processing tools.