https://github.com/ssi-dk/cd-mrg-bruker

Scripts and documentation for Bruker software
https://github.com/ssi-dk/cd-mrg-bruker

Last synced: 3 days ago
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Scripts and documentation for Bruker software

• Host: GitHub
• URL: https://github.com/ssi-dk/cd-mrg-bruker
• Owner: ssi-dk
• License: gpl-3.0
• Created: 2023-11-14T20:04:01.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-01-16T16:10:22.000Z (10 months ago)
• Last Synced: 2024-01-17T00:34:56.197Z (10 months ago)
• Language: VBScript
• Size: 88.9 KB
• Stars: 0
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# CD-MRG-Bruker

Code and documentation pertaining to Bruker software for LC-MS data. 

## Source 

Metabolomics Research Group, department of Congenital Diseases at Statens Serum Institute (SSI) Denmark.

## Bruker Data Analysis 

Tasks in **Data Analysis (DA)** can be automated using the Visual Basic Script (VBS) api. 

To process loaded files in DA using scripts,

1) click *Method > Open Script Only ...*;

2) Click *Method > Run*

### Scripts

These scipts require files to be imported to the DA *Analysis List*. For >10 files, see []

- [Export Bruker files to mzML](https://github.com/ssi-dk/CD-MRG-Bruker/blob/main/DataAnalysis/exportMzML.dascript) 

- [Recalculate linespectra from profile spectra](https://github.com/ssi-dk/CD-MRG-Bruker/blob/main/DataAnalysis/recalc_linespectra.dascript) 

### Methods

These methods are intended to be used with *ProcessWithMethod* for batch processing as described below

- [Recalculate linespectra from profile spectra]()

- [Export to mzML]()

**NOTE** If the export fails you may not have write privileges in the target directory, or the target directory does not exist.

### Batch processing

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*. )

![proc_with_method](readme_assets/processwithmethod.PNG)

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*. 

#### Editing the method file

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. 

##### `recalc_linespectra.m` parameters

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

- ![compass param](readme_assets/compass_parameters_sumpeak.PNG)

##### `export_to_mzml.m`

Open the method file in MethodEditor. To change the output directory, open the script by clicking *Method > Script*