Converting Thermo RAW Files to SORCERER™ Compatible Input Files

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While the Sorcerer comes with a built-in converter for Thermo mass spectrometer RAW files, for full compatibility with searching Thermo data on Sorcerer we recommend using your Windows PC and the freely available program msconvert from ProteoWizard to convert RAW files into mzML/mzXML files which can be searched by the Sorcerer.

The instructions below will cover how to install and use msconvert to convert RAW files into mzML files. 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 RAW files into mzML files with msconvertGUI.

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 RAW files you want to convert. Selecting multiple files 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 files 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, and TPP compatibility 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 ‘Peak Picking.’ The options for Peak Picking may be left at their default values. Then click Add so it gets added to the Filter box. peakPicking MUST be the first filter in the list in order to use the Thermo supplied centroiding algorithm as the vendor DLLs only operate on raw untransformed data. Drag the peakPicking filter to the top of the list of filters if it’s not already there. In the screenshot below, you can see peakPicking is above titleMaker.

6. Click the arrow next to ‘Save Preset’ and choose the option ‘Save as defaults for Thermo RAW 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 ‘Thermo RAW Defaults‘ preset option to automatically select these options.

7. Once you are done selecting the RAW 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 RAW 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.