LiRTMaTS - Liverpool Retention Time Matching Software

Introduction

Untargeted metabolomics studies routinely apply liquid chromatography-mass spectrometry (LC-MS) to acquire data for hundreds or low thousands of metabolites and exposome-related (bio)chemicals. The annotation or higher-confidence identification of metabolites and biochemicals can apply multiple different data types (1) chromatographic retention time, (2) the mass-to-charge (m/z) ratio of ions formed during electrospray ionisation for the structurally intact metabolite or (bio)chemical and (3) fragmentation mass spectra derived from MS/MS or MSn experiments.

Chromatographic retention time is a complementary data type when compared to m/z and MS/MS data. Method-specific retention time (RT) libraries can be constructed by the analysis of pure metabolite standards applying the same assay and reporting the detected RT. The library RT can be compared to RT of a metabolite detected in an untargeted metabolomics study to aid in the annotation or identification of metabolites. The LiRTMaTS is a Python package and easy-to-use software for matching RTs detected in an untargeted metabolomics study to RTs present in a RT library. Any RT library can be applied though this RT library should be specific to the LC-MS assay applied (RT libraries are not transferable across different LC-MS assays). All matches within a RT range are reported.

Installation

Source

Install directly from GitHub:

pip install git+https://github.com/wanchanglin/lirtmats.git

PyPI (Coming soon)

To install from PyPI via pip, use the distribution name lirtmats:

pip install lirtmats

This is the preferred installation method.

Use the following to update if lirtmats has been installed before:

pip install lirtmats --upgrade    # upgrade to the newest version

Conda (Coming soon)

lirtmats is in Bioconda channel and use the following to install or update for conda:

conda install -c bioconda lirtmats

Use the following to update if lirtmats has been installed before:

conda update -c bioconda lirtmats       # upgrade to the newest version

Usages

lirtmats provides command line and graphical user interfaces for the end users.

$ lirtmats --help
Executing lirtmats version 1.0.0.
usage: lirtmats [-h] {cli,gui} ...

Retention Time Matching of LC-MS data

positional arguments:
  {cli,gui}
    cli       Retention Time Matching in CLI.
    gui       Retention Time Matching in GUI.

options:
  -h, --help  show this help message and exit

Command line interface (CLI)

Use the follow command line to launch CLI mode: :

$ lirtmats cli <arg_lists>

The following is an example:

lirtmats cli \
  --input-data "./data/df_pos_3.tsv" \
  --input-sep "tab" \
  --col-idx "1, 2, 3, 4" \
  --rt-path "" \
  --rt-sep "tab" \
  --rt-tol "5.0" \
  --ion-mode "pos" \
  --save-db \
  --summ-type "xlsx" \

Graphical user interface (GUI)

$ lirtmats gui

Links

• Documentation: Read the Docs

Authors

• Wanchang Lin (Wanchang.Lin@liverpool.ac.uk), The University of Liverpool
• Warwick Dunn (Warwick.Dunn@liverpool.ac.uk), The University of Liverpool