Using msconvert with PepFoot

Windows

If you are using PepFoot on Windows then you simply need to install the ProteoWizard application along with its dependencies. When you first use the File Convert button in PepFoot, you will be asked to select the location of msconvert.exe, which should be in your Program Files > Proteowizard folder. PepFoot will then convert any selected files to the .mz5 format using our standard settings.

Important: If you have updated your ProteoWizard (and msconvert) installation then you will need to make sure PepFoot is using the correct one, see Updating Proteowizard location

Linux and MacOS

If you are using a Linux/MacOS system and want to convert vendor RAW files then you will need to install the Windows version of ProteoWizard with something like WINE or Docker. We recommend using the Docker instructions given by the ProteoWizard developers. You can then use a custom shell script to correctly parse msconvert settings, an example script is found here. You will need to give this file executable properties, chmod +x docker-msconvert.sh. When you first use the File Convert button in PepFoot, you wil be asked to select the location of this file. Note: PepFoot will only process this script correctly if it is launched from a terminal

Important: If you have updated your shell script location then you will need to make sure PepFoot is using the correct one, see Updating Proteowizard location

To use this script outside of PepFoot, add it to your local bin /usr/local/bin/ (cp ./docker-mscovert.sh /usr/local/bin/msconvert) and run it with standard arguments, e.g. msconvert data.RAW --zlib --filter "zeroSamples removeExtra" --mz5. This script may also function with other software dependent on msconvert

Updating Proteowizard location

After updating your local copy of Proteowizard (and msconvert), you will need to change this in PepFoot (regardless of whether you have reinstalled PepFoot). To do this, you must reset this value in the pepFoot.ini settings file, follow the instructions below:

Windows

1. Close PepFoot completely, otherwise any changes will not take effect.
2. Go to your local user app settings directory, C:\Users\%USERPROFILE%\AppData\Roaming\pepFoot (either copy this directly into your Windows Explorer address bar or replace %USERPROFILE% with your user name)
3. Open the pepFoot.ini file with a text editor.
4. Under the [General] heading, look for the line beginning with pwiz and delete this line.
   • For example, mine says pwiz=C:/Program Files/ProteoWizard/ProteoWizard 3.0.20310.42ec66a95/msconvert.exe
5. Save and close the file.
6. Open PepFoot and follow the instructions above

Linux and MacOS

1. Close PepFoot completely, otherwise any changes will not take effect.
2. Go to your local user app settings directory, ~/.config/pepFoot (either copy this directly into your Windows Explorer address bar or replace %USERPROFILE% with your user name)
3. Open the pepFoot.ini file with a text editor.
4. Under the [General] heading, look for the line beginning with pwiz and delete this line.
   • For example, mine says pwiz=~/.local/bin/docker-mscovert.sh
5. Save and close the file.
6. Open PepFoot and follow the instructions above