Transition Extraction, Training and Execution Harness for flipR

This project provides an execution harness including transition extraction from mzML files, automatic model training and selection based on the flipr project.

To use it on Linux systems with parallelized training, please see the flipr-trainer.

flipR (Fragment-based Lipid Intensity Prediction) predicts MS-platform specific lipid fragment profiles that simplify the selection of optimized collision energies for custom lipid transition libraries with LipidCreator in conjunction with Skyline.

The Maven site with JavaDoc is available here.

Table of Contents

• Building the project and generating client code from the command-line
• Running the application

Building the project and generating client code from the command-line

In order to build the client code and run the unit tests, execute the following command from a terminal:

./mvnw install

This generates the executable JAR file for reading and mapping of transition lists, mapping files and mzML transition extraction.

The generated JAVA code is available in a jar archive below the target directory:

1. flipr-transition-extractor-<VERSION>.jar

Running the application

If you want to run the application from the command line, change to the target folder after building the project. Then enter the following command:

java -jar flipr-transition-extractor-1.0.9.jar

This will print all possible arguments for the transition extractor.

Note	You need to have the flipr R package installed before running the transition extractor.

The flipr-trainer project shows how to use the transition extractor.