`config`#

The purpose of this command is to take a peak list in .csv format that the user provides and translate it to the YAML format supported by this package.

PTR-TOF mass spectrometry generates data that might be interpreted in a variety of ways depending on the experiment set-up. The reagent that is used as the ionization source, as well as the calibration of the instrument, might both affect the exact m/z value at which a compound’s signal is detected. For this reason, the user must provide a configuration file to guide the data processing. This config file is in a readable YAML format that looks like this:

name: example-peak-list
author: Johnny Appleseed
peak-list:
-   mf: H2O
    smiles: O
    mass-range:
        min: 19.016
        max: 19.02
-   mf: C2H2
    smiles: C#C
    mass-range:
        min: 27.021
        max: 27.025

There are 4 different inputs to describe each peak in the mass spectrum:

mf – molecular formula
smiles – SMILES (Simplified Molecular Input Line Entry System) string, provided for substructure matching purposes. (learn more)
mass-range / min – m/z lower bound on peak integration
mass-range / max – m/z upper bound on peak integration

Creating this configuration file is made easy by the config command. The user must provide a .csv (or .feather) FILE in any of the 3 following formats:

1. Ion Style (pass `--ion` flag)#
ion	min	max
C6H7+	79.048	79.06

2. Molecular Formula Style (don’t pass a flag)#
mf	min	max
C6H6	79.048	79.06

3. SMILES Style (pass `--smiles` flag)#
mf	smiles	min	max
C6H6	CC=C=CC#C	79.048	79.06

Note on Molecular Identifiers

To read about the thoughts that went into these three formats, and their key differences, see more.

Also name and author can be passed directly to the config command using the --name and --author options.

Below is an example command where ion_peaks.csv, a file in the format of #1 above, is transformed into a YAML peak list saved to my_peak_list.yml.

$ tofspec config -o my_peak_list.yml --ion ion_peaks.csv

config#

`config`#