APL to MGF Converter

This program allows you to convert MaxQuant APL peaklist files to compatible MGF peaklist files. Ensure that the APL files are generated accurately by running MaxQuant and Andromeda against a suitable sequence database reflecting the sample under study i.e., do NOT limit the search to contaminants only in order to speed up the search.

• Run setup.exe (note you can safely ignore warnings such as publisher could not be verified or subsequent security warnings).
• Click Install.
• Microsoft's .NET framework 4.5.1 will be downloaded and installed if missing.
• The program will create a shortcut on the desktop and the GUI will appear if installation is successful.
• Drag-and-drop APL files from Windows Explorer onto the empty window or choose Add Files (include all apl files including secpep).
• Choose Select to indicate the location of Maxquant's TXT folder (evidence, allpeptides, msmsScans etc.).
• Demixing of chimeric spectra is supported if the "Use original peaklist for secondary peptides" is checked (default).
• The peaklists will be written to mgf files using the original MS raw file name if "Write to original MS acquired file name" is checked (default). 
• Select the fragment ions type appropriate for your MS instrument (if in doubt e-mail kapp@wehi.edu.au).
• Click Process to convert APL files to MGF. Files will be written to the same location.
• Select Cancel in order to interrupt the conversion process.
• Select Quit to close the application.

Download the setup.exe file

Tools

• mascotResultDownload
• Command line tools