integrate-peaks#
The purpose of this command is to take a .csv (or .feather) of raw mass spectrometry data, and a peak list in the accepted YAML format, and output an integrated time series of compounds.
From the raw format discussed on the load guide, to a table that looks like this:
mf or smiles |
mf or smiles |
… |
|
|---|---|---|---|
timestamp 1 |
# |
# |
# |
timestamp 2 |
# |
# |
# |
… |
# |
# |
# |
The integrate-peaks command requires that the user specifies
a peak list with the -c, --config argument. Beyond that, their are some optional arguments to describe
your input and customize your output. Pass -ts, --tscol with the name of your timestamp column if there
is one in your input file. Pass -i, --ignore with the names of any metadata columns that you want to be
passed from input to output. And choose whether you want your compound columns to be denoted by molecular
formula (-col=mf) or SMILES (-col=smiles). As always, specify your output path with -o, --output.
Below is an example command where raw_data.csv, is integrated based on the peaks specified in my_peak_list.yml and saved to integrated_data.csv.
raw_data.csv has a timestamp column named ‘Time’, and integrated_data.csv will have columns denoted by molecular formula.
$ tofspec integrate-peaks -o integrated_data.csv -ts Time -c my_peak_list.yml -col=mf raw_data.csv
Important
The purpose of the -col argument is not just stylistic. It plays a role in the ultimate label-ing
of data which is discussed in the next command.