Converting Bruker Ion Mobility Data to SORCERER™ Compatible Input Files

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The instructions below will cover how to install and use msconvert to convert Bruker Ion Mobility data TDF files into mzML files which can be analyzed on the SORCERER™. There are two ways to use msconvert, on the command line or through the GUI. This tutorial will cover using the GUI version.

 

Installing msconvert on a Windows PC

1. Download the latest Proteowizard package from: http://proteowizard.sourceforge.net/download.html. For the Platform, select: Windows XX-bit installer (able to convert vendor files…), XX being either 64-bit or 32-bit depending on your Windows OS version. Click their agreement check box and download the file.

2. Save the pwiz-setup-X.X.XXXX-XXX.msi file to any location on your Windows computer.

3. Double click on the pwiz-setup-X.X.XXXX-XXX.msi to run their installer

 

How to convert Bruker TDF files into mzML files with msconvert GUI

1. Click the Windows Start button and navigate to All Programs > ProteoWizard X.XX.XXXX. Click on MSConvert.

2. Use the Browse button to select all the Bruker TDF data directories you want to convert. Selecting multiple TDF directories and clicking Open will automatically add them to the list which you can see in the box below the Add/Remove buttons. If you are browsing for TDF directories one by one, you will need to click the Add button after browsing and opening so they get added to the list box.

3. You may change the ‘Output Directory’ if you want the mzML files to go to a specific location.

4. For the Options, use the drop down bar to change the ‘Output format’ to mzML.  Verify the boxes next to Write Index, Use zlib compression, TPP compatibility, and Combine ion mobility scans are CHECKED. Binary encoding precision should be 64-bit, Package in gzip can be left unchecked.

5. Under Filters, use the drop down box and select ‘Scan Summing.’ The options for Scan Summing may be left at their default values. Then click Add so it gets added to the Filter box.

6. Click the arrow next to ‘Save Preset’ and choose the option ‘Save as defaults for Bruker TDF data.’ When you use msconvert in the future, you can just use the Presets drop-down menu found in the lower left-hand side to select the ‘Bruker TDF Defaults‘ preset option to automatically select these options.

7. Once you are done selecting the TDF files, Options, and Filters, verify your window looks similar to the window below, then click the Start button to begin the conversion process.

8. Depending on the number and size of your TDF files, the program may take some time to finish. You will see a Finished message next to each input file in the Conversion Progress window once the process is completed. If any conversion failed, see the message box for clues. 

9. You may now copy the mzML files you created to the SORCERER data folder and submit them for a search.