LA-ICPMS Converter Module

The Converter for LA-ICP-MS data, can read LA-ICP-MS mapping data natively and generate intensity and standard maps for XMapTools (Markmann et al 2024).

Main steps to import LA-ICP-MS data

  • Import files including a data file from the mass spectrometer containing time stamps and intensity data, and optionally a log file from the laser system
  • Adjust the time shift to synchronise the two data sets
  • Generate a log file (if not available) using the Log Generator module
  • Extract integrations for each measurement
  • Apply a background correction using one of the available functions
  • Select primary standard(s) and fit to generate a primary standard intensity function
  • Select secondary standard(s) and check the quality of standardisation for each element selected as an internal standard
  • Generate maps using the interpolation method described in Markmann et al. (2024) for unknowns and standards, and export map files.

Step 1: Load datafile(s)

The import tools are located at the top of the module. The data format can be selected from the first drop down menu and the file format (single or multiple) from the second drop down menu. The data from a measurement session can be contained in a single file or multiple files. If multiple files are selected, it is recommended that you select the last file first and then hold MAJ while selecting the first file, not vice versa. For the laser, deselect the log file option if no compatible log file is available. In this case, the Log Generator module will appear when the Load Datafiles button is pressed.

Once appropriate options have been selected, press the Load Datafiles button to select: (1) a single data file from the mass spectrometer containing timestamps and intensity data (e.g. Data.csv) or multiple files (see warning above), and (2) if the Log File option is enabled, immediately after a corresponding log file (e.g. Log.csv) from the laser system (tested with RESONETICS only).

Step 2: Adjust time shift

The value of the time shift can be adjusted to synchronise the data file with the log file. In the main figure, the total signal is plotted together with the laser on/off signals given in the log file (vertical red lines). The shift value is automatically adjusted by XMapTools when the data is imported. If necessary, adjust the value until both signals are synchronised.

Step 3: Extract integrations & plot data

Once the value of the time shift is optimised, press the Extract Integrations button to automatically extract all the analyses listed in the log file. They should appear in the Integration tree menu on the left of the window after extraction.

Step 4: Apply background correction

The integrations for fitting a background correction are automatically selected for each measurement. They are listed in a tree menu (integration menu) located on the left and can be plotted by selecting an item under the category Background.

Display/edit integrations for background

To view and edit integrations, select the first measurement in the tree menu. The display is automatically adjusted to zoom in on the selected integration. If you select a different measurement in the tree menu, the integration will be displayed in the centre of the plot. The program automatically excludes a fraction of sweeps at the beginning and at the end of each background measurement (default value is 10 %). This value can be changed manually if required. It is also possible to manually edit the duration of an integration by changing the limit values available as Sweep (min and max).

Background interpolation

Select a method for fitting the background in the BACKGROUND section below the plot. It is recommended to display the signal Raw_Sum and to adjust the display to show the entire background signal. The following functions are available: (1) linear, (2) polynomial, (3) step function, (4) spline. Step function is recommended for background correction. Press the button Apply to apply the background correction. You cannot change the background correction once it has been applied.

Step 5: Select primary standard(s)

The background-corrected (BackCorr) signal is displayed when a background correction has been applied. Corrected data are available from the Plot menu. Select the measurement to be used as the primary standard from the PRIMARY STANDARD drop down menu. The integration name should match the name of a standard file containing the composition of this standard (e.g. NIST612 or GSD-1g). It is also possible to add custom files using the options available in the lower left panel, but this process must be repeated each time the converter is used. Integrations can be edited using the same strategy as for background integration (see above).

Then select an interpolation method. A spline function is usually the best method to approximate instrument drift during the measurement, especially when reconstructing maps (Markmann et al. 2024). A step function can also be used in some cases, but this can result in sharp transitions between lines in the final map. Press the Apply button to validate and interpolate the primary standard signal. If the standard is not automatically recognised, a window will open with a list of all available standards. It is possible to define additional interpolations to be used as primary standards. After pressing the Apply button it is possible to define a new interpolation for the same material or for a different material by selecting the Yes option. If you do not wish to define any further interpolations to be used as primary standards, select No (Continue).

Step 6: Select and check secondary standard

Select the measurements to be used as the secondary standard using the drop down menu under SECONDARY STANDARD. Integrations can be edited using the same strategy as for background integration and primary standard (see above). Use the Int. Std drop down menu to select an element to be used as a reference for calculating the composition of the secondary standard. This choice has no effect at this stage on the map calibration performed in XMapTools (another element can be used). But here it is possible to quickly check the calibration using the secondary standard for several elements used as internal standard.

Step 7: Generate map files

Maps can be generated from raster measurements after background correction, adjustment of the primary reference material(s) and checking of the secondary reference material(s). Use the drop down menu in MAPS (SCANS) to select the raster measurements to be used to construct the map. Integrations cannot be edited. Press the Apply button to validate and generate the maps. Three buttons become available.


Markmann, T.A., Lanari, P., Piccoli, F., Pettke, T., Tamblyn, R., Tedeschi, M., Lueder, M., Kunz, B., Riel, N., and Laughton, J. (2024). Multi-phase quantitative compositional mapping by LA-ICP-MS: analytical approach and data reduction protocol implemented in XMapTools. Chemical Geology646, 121895.

Documentation in XMapTools

The last version of the documentation is provided below:

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