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freequant
Sarah Haynes edited this page Nov 8, 2019
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Quantify and compare the protein nature and spectral counting values between 2 or more Philosopher results.
philosopher freequant [files]
--dir
Folder path containing the raw files
--isolated
Use the isolated ion instead of the selected ion for quantification
--ptw
Specify the time windows for the peak (minute) (default 0.2).
--tol
M/Z tolerance in PPM (default 10).
Use spectra information from all mz files and, based on the peptide identifications, extract the given intensities. The resulting intensities will be stored inside the workspace, there is no output from this command.
philosopher freequant --dir mz/