.NET version of Raxport

Raxport is a simple program which extracts scans from raw files generated by mass spectrometers from ThermoFisher. It supports both Orbitrap and IonTrap scans. However, the generated .FT1 or .FT2 files will include charge information only if the scan is from an Orbitrap. Currently, only MS1 and MS2 scans are supported.

Run it on Windows

.\Raxport.exe -i 'input path' -o 'output path' -j 'threads number'

Run it on Linux or MAC

./Raxport -i 'input path' -o 'output path' -j 'threads number'

To split 20,000 scans per .FT2 file

./Raxport -i 'input path' -o 'output path' -s 20000 -j 'threads number'

Scans in Generated .FT1 File

The format of .FT1 is shown in the following picture. All chunks are split by tabs.

• The first "H" line contains software information.
• The second "H" line contains column names for peaks.
• The third "H" line contains the instrument model.

Each scan has a scan header and a peaks information table.

• The "S" line in the scan header contains the scan number and TIC (total ion current).
• The first "I" line contains the retention time.
• The second "I" line contains the scan type.
• The third "I" line contains the scan filter.

Scans in Generated .FT2 File

The format of .FT2 is shown in the following picture. All chunks are split by tabs.

• The first "H" line contains software information.
• The second "H" line contains column names for peaks.
• The third "H" line contains the instrument model.

Each scan has a scan header and a peaks information table.

• The "S" line in the scan header contains the scan number, precursor m/z, and TIC (total ion current).
• The "Z" line contains the precursor charge, precursor mass, and other precursor charges and m/z values.
• The first "I" line contains the retention time.
• The second "I" line contains the scan type.
• The third "I" line contains the scan filter.
• The "D" line contains the scan number of the precursor.

Compile it in Visual Studio

Raxport.net is developed under .NET 8 and relies on ThermoFisher.CommonCore.RawFileReader.dll and ThermoFisher.CommonCore.Data.dll from RawFileReader. You can clone this project and compile it in Visual Studio. See the note.md for additional details.