Code and documentation pertaining to Bruker software for LC-MS data.
Metabolomics Research Group, department of Congenital Diseases at Statens Serum Institute (SSI) Denmark.
Tasks in Data Analysis (DA) can be automated using the Visual Basic Script (VBS) api.
To process loaded files in DA using scripts,
- click Method > Open Script Only ...;
- Click Method > Run
These scipts require files to be imported to the DA Analysis List. For >10 files, see []
These methods are intended to be used with ProcessWithMethod for batch processing as described below
NOTE If the export fails you may not have write privileges in the target directory, or the target directory does not exist.
DA is not designed to handle multiple files; loading more than 10-20 files typically causes the program to freeze. If you want to process multiple data files (e.g. a batch) using DA, the best option is to use the ProcessWithMethod program which you can start in DA by clicking Tools > ProcessWithMethod. (ProcessWithMethod is a Compass AutomationEngine script. )
In ProcessWithMethod you load a method file that defines operations applied to all files in the Analysis list; click Select to add files to the Analysis list for processing. Click process to start the analysis; you cwill see the progress in the Compass DA ProcessQueuer.
Open the Bruker Compass MethodEditor app and load the method file by clicking Method > Open.
Click Method > Script to view the commands/methods/algorithms that will be executed for each file when the method is run. Click Method > Parameters to view and set the parameters associated with commands/methods.
Open the method file in MethodEditor. To change the parameters for the Sum Peak algorithm used to compuute the line spectra (i.e. the spectral centroids of the profile spectra), open the file recalc_linespectra.m and then click Method -> Parameters and then click on the MassList > Sum Peak section as shown below
Open the method file in MethodEditor. To change the output directory, open the script by clicking Method > Script