This collection of scripts is the training harness for CE-dependent, relative fragment intensity prediction models for LipidCreator. If you need support to set the harness up, please create a GitHub issue or contact us at https://lifs.isas.de/support

This project uses flipr and the flipr-transition-extractor.

The code of flipr trainer has been developed and tested on Ubuntu Linux 16.04 and 18.04. It should work on other Linuxes as well, but you may have to adapt the following commands for package installation to fit to your distribution.

• Java JRE > 1.8
• SDKMAN

curl -s "https://get.sdkman.io" | bash
sdk install groovy

• Asciidoctor + Fonts

sudo apt install asciidoctor fonts-liberation

• Asciidoctor-PDF

sudo gem install asciidoctor-pdf -pre
sudo gem install prawn --version 2.1.0
sudo gem install prawn-svg --version 0.26.0
sudo gem install prawn-templates --version 0.0.4

• R >=3.5, see https://www.r-project.org/ for installation instructions
• devtools package (to install packages from github)
• Viridis package (color scale used for global overview plots over all instances)
• flipR package (Requires R>=3.5, for model training and selection)
• all other dependencies should be installed automatically

install.packages(c("devtools","viridis"))
library(devtools)
devtools::install_github("lifs-tools/flipr")

Please note that the model training has been tested under Ubuntu 18.04 Linux only. You will need to download the mzML files from the MetaboLights studies MTBLS1333 (qex-hf) and MTBLS1334 (qtof) to the respective measurements folders. E.g. measurements/QExHF03 for the MTBLS1333 data, and measurements/QTof folder for the MTBLS1334 data.

To run the model training for one of the two platforms (termed INSTANCE), proceed as follows:

./run-fip.sh <INSTANCE>

where <INSTANCE> can be either qex-hf or qtof. This will also create overview plots for all trained models and the supplementary material pdf file with selected plots on the model performance for each molecule and group combination.

The config folder contains a <INSTANCE>.properties file and an <INSTANCE>.R which set common properties for the model training with flipR and for the optimization bounds. The file common.sh defines common functions and BASH variables used by the other scripts. The NTHREADS will be set to half of the number of logical CPU cores available on your system. You can also set it lower, if you want to. The file also defines the command that runs the transition extractor on the mzML files, which in turn executes flipR (CMD).

The mappings folder contains subfolders for each <INSTANCE>, e.g. qex-hf. This folder may contain multiple .tsv files with the following structure:

FileId	Mode	Name	Instrument	MoleculeGroup	PrecursorName	PrecursorAdduct	PPMS	File	Group	Date
QExHF03_NM_0000125	HCDoptimization_NegMode_2min_30K	PGF2alpha{d4}	MS:1002523	PGF2alpha	PGF2alpha{d4}	[M-H]1-	5|10	measurements/QExHF03/QExHF03_NM_0000125.mzML	125	Jul-27-2018

Each line represents one measurement. The line maps a file id, the molecule name, instrument cv term, precursor name, adduct, and the PPMS to use for signal extraction to the mzML file for that measurement. A Group can be provided to be able to disambiguate multiple measurements for the same molecule and similar conditions.

Measurements are stored below the measurements folder. The name of the subfolders is arbitrary, but needs to be part of the path referencing the mzML files from the base directory (the directory containing this README file).

The transitions folder contains .tsv transition files that were created with LipidCreator in "development mode". To do so, you currently need to start LipidCreator.exe from the command line

• via cmd on Windows as LipidCreator.exe dev, or
• via shell with mono LipidCreator.exe dev on Linux (this requires the latest mono version installed, tested with mono 6.8).

This ensures that lipid PrecursorNames are written out in a format that can be mapped back into LipidCreator from the ce parameter file that flipR creates after the model training and selection process.

The MoleculeGroup, PrecursorName and PrecursorAdduct are joined with the columns in the mapping file to generate the list of transitions to extract from the mzML file.