Quick start

Installation

IsoGroup requires Python 3.7 or higher. If you do not have a Python environment configured on your computer, we recommend that you follow the instructions from Anaconda.

Then, open a terminal (e.g. run Anaconda Prompt if you have installed Anaconda) and type:

pip install isogroup

You are now ready to start IsoGroup.

If this method does not work, you should ask your local system administrator or the IT department “how to install a Python 3 package from PyPi” on your computer.

Alternatives & update

If you know that you do not have permission to install software systemwide, you can install IsoGroup into your user directory using the --user flag:

pip install --user isogroup

If you already have a previous version of IsoGroup installed, you can upgrade it to the latest version with:

pip install --upgrade isogroup

Alternatively, you can also download all sources in a tarball from GitHub, but it will be more difficult to update IsoGroup later on.

Usage

Command Line Interface

IsoGroup can be executed from the command line interface (CLI) to perform either untargeted isotopic grouping or targeted annotation.

You can now use two separate command-line executables depending on your needs:

Targeted annotation using a database:

isogroup_targeted [command line options ]

Here after the available options with their full names are enumerated and detailed.

usage: isogroup_targeted [-h] -t TRACER -D DATABASE -ppm PPM_TOL -rt RT_TOL -o
                         OUTPUT [-v]
                         inputdata

Positional Arguments

inputdata: input dataset file

Named Arguments

-t, --tracer

the isotopic tracer (e.g. “13C”)

-D, --database

path to database file (csv)

-ppm, --ppm_tol

m/z tolerance in ppm (e.g. “5”)

-rt, --rt_tol

retention time tolerance in sec (e.g. “10”)

-o, --output

path to generate the output files

-v, --verbose

enable verbose logging

Default: False

IsoGroup automatically carries out either untargeted isotopic grouping or targeted annotation of mass features

Warning

The annotation and grouping options must be carefully selected to ensure reliable interpretations of labeling data, as detailed in the Tutorials.

Untargeted isotopic grouping:

isogroup_untargeted [command line options]

Here after the available options with their full names are enumerated and detailed.

usage: isogroup_untargeted [-h] -t TRACER -ppm PPM_TOL -rt RT_TOL
                           [--max_atoms MAX_ATOMS] [-k KEEP] -o OUTPUT [-v]
                           [--unlabeled UNLABELED]
                           [--fully_labeled FULLY_LABELED]
                           inputdata

Positional Arguments

inputdata: input dataset file

Named Arguments

-t, --tracer

the isotopic tracer (e.g. “13C”)

-ppm, --ppm_tol

m/z tolerance in ppm for grouping (e.g. “5”)

-rt, --rt_tol

rt tolerance in sec for grouping (e.g. “10”)

--max_atoms

maximum number of tracer atoms in a molecule (e.g. “20”). OPTIONAL

-k, --keep

strategy to deduplicate overlapping clusters: “longest”, “closest_mz”, “both”, “all”. OPTIONAL

Default: 'all'

-o, --output

path to generate the output files

-v, --verbose

enable verbose logging

Default: False

--unlabeled

Unlabeled sample name

--fully_labeled

Fully labeled sample name

Library

IsoGroup is also available as a library (a Python module) that you can import directly in your Python scripts:

import isogroup