1. Install MSFileReader from Thermo (see below)
2. Ensure your regional settings parameters are '.' for the decimal symbol and ',' for the list separator
3. Download the zip archive and unzip it
4. See last section of this page to know how to use the tool

MSFileReader is the standard library used by raw2mzDB to access Thermo raw files.

1. Create a Thermo account at https://thermo.flexnetoperations.com/control/thmo/RegisterMemberToAccount
2. Once you are registered, you can download MSFileReader 3.0 from https://thermo.flexnetoperations.com/control/thmo/login (you will need to enter your login information)
3. Go to the “Utility Software” section to download the file
4. Unzip it, right click on the executable and left click on “Run as Administrator”
5. Install it with defaults settings
6. Install both 32-bit and 64-bit versions if possible (it will install all necessary c++ redistribuables)

Open a command line window in the directory containing raw2mzdb.exe
Type:
raw2mzdb.exe -i <rawfilename> -o <outputfilename>
By defaut, the raw file will be converted in the “fitted” mode for the MS1 (MS2 is often in centroid mode and can not be converted in fitted mode). If the MS2 (or superior) are acquired in high resolution (i.e in profile mode), you could specify that you want to convert several MSs in the required mode: raw2mzdb.exe -i <rawfilename> -o <outputfilename> -f 1-2 will try to convert MS1 to MS2 in fitted mode.

There are two other available conversion modes:

1. “profile”, the command line is then: raw2mzdb.exe -i <rawfilename> -o <outputfilename> -p 1 (means you want profile mode for MS1, others MS will be stored as they were stored in the raw file)
2. “centroid” : raw2mzdb.exe -i <rawfilename> -o <outputfilename> -c 1 (means you want centroid mode for MS1, others MS will be stored as they were stored in the raw file)