Tools for bile acid identification

BART: a transferrable LC retention time library for bile acids

BART is a Java program to predict gradient retention times of bile acids on different LC-MS instruments based on isocratic retention modeling.
Currently the database contains 272 bile acids measured under the following LC condition:
Column: Waters BEH C18 (2.1 mm × 100 mm, 1.7 µm)
Mobile phase A: 7.5 mM ammonium acetate (adjusted to pH 4.9 using acetic acid) in water
Mobile phase B: ACN
Flow rate: 0.45 mL/min
Column temperature: 45 ℃

Download BART

Program: for Windows 64, Mac OS
Library: c0, c1 and c2 parameters in the quadratic solvent strength model (QSSM) for 272 bile acids ( txt )
User Manual (PDF)
Test data: an example dataset ( zip )
Data for publication: validation datasets on five LC-MS systems ( zip )

Quick Start with Test Data

After extracting the contents of program and test data, change the file paths in the .bat file in the “test_data” folder according to their actual location and double click to run it. The output should be same as the “predictedRT_example.tsv” in the “test_data” folder. See User Manual for more details.

BAFinder: unknown identification from MS/MS

BAFinder is a program developed for the unknown bile acid identification from LC-MS/MS data in both positive and negative modes. It was developed in Java (jdk 15.0.1) with a graphical user interface (GUI) using the Open Source IDE Eclipse. BAFinder takes the alignment and peak list generated from XCMS (csv) and MS/MS spectra (MGF), searches them against a MS/MS reference library (MSP), a build-in characteristic feature (e.g. product ion or neutral loss) query list and an optional retention time library (txt) within user-defined m/z and RT tolerance, and exported the annotation summary (csv), processing details (csv) and representative MS/MS spectra (MGF) into an output folder.

New: BAFinder 2.0 is comming!

BAFinder 2.0 offers new functions to annotate amino-acid conjugated bile acids other than glycine and taurine.
For internal validation, please go to the following site to download the library, software and test data:
https://github.com/BAFinder/bafinder.github.io/tree/BAFinder-2.0

Download BAFinder 1.0

BAFinder software
If you don’t want to install java, please download the packaged program for Windows64 or macOS system.(~70 MB)
If you already have jre 15.0.1 or later installed, or don’t mind installing java on your system, please download the jar file for Windows or macOS system. (~20 MB).

The following resources are also available for download:
User Manual (PDF)
MS/MS library for bile acids (MSP, including 84 bile acids, developed using QE-HFX in positive ESI mode at NCE 45 and negative ESI mode at NCE 60)
Test data (zip, example for input and output files of a human plasma dataset, with library included)

Citation

If you use BAFinder software or libraries in your published work, please cite the BAFinder paper:
BAFinder: A Software for Unknown Bile Acid Identification Using Accurate Mass LC-MS/MS in Positive and Negative Modes
DOI:10.1021/acs.analchem.1c05648

Contact

If you have any question about BAFinder, please contact Dr. Yan Ma (mayan@nibs.ac.cn).