Using the Command Line

Use the --help argument to get a list of arguments. For example, on Windows:

CMD.exe --help

At minimum, the --idt (the identification file) and --rep (the spectra file repository) arguments must be specified.

If you want to normalize results or perform Bayesian statistical analysis using the command-line, you must create an experimental design TSV file and place it in the directory with your spectra files (see Experimental Design wiki page).

For boolean (true/false) parameters, an absent flag means "false" and a present flag means "true".

For example, the chg parameter will be set to true here:

CMD.exe --idt "C:\MyFolder\msms.txt" --rep "C:\MyFolder" --ppm 5 --chg

The chg parameter will be set to false here:

CMD.exe --idt "C:\MyFolder\msms.txt" --rep "C:\MyFolder" --ppm 5

false is the default state for all of FlashLFQ's Boolean parameters.

Processing Thermo .raw files

If you would like to process Thermo .raw data files directly, you must agree to the Thermo license. This is accomplished by creating a text file with the name "LicenseAgreements.toml" with the text below. This file should be placed in the same directory as the executable program.

HasAcceptedThermoLicence = true

Windows

To use the FlashLFQ standalone command-line version, run the "CMD.exe" program with command-line arguments.

Preferably, when specifying a filepath, use the absolute file path inside of quotes.

Example:

CMD.exe --idt "C:\MyFolder\msms.txt" --rep "C:\MyFolder" --ppm 5 --chg

Linux

FlashLFQ is best run in Linux via .NET Core. You can also use Mono, though historically there have been RAM issues. You can run the .NET Core version of FlashLFQ with the "dotnet CMD.dll" command. You will likely not be able to open Thermo .raw files in Linux; you should convert them to .mzML before quantifying with FlashLFQ.

Example:

dotnet CMD.dll --idt "/home/myfolder/msms.txt" --rep "/home/myfolder" --ppm 5 --chg