TICQ: Total Ion Current Quality Assessment of Mass Spectrometry Spectral Data

Introduction

TICQ is a R package that allows you to quickly assess mass spectrometry (MS) spectral data for sample quality and instrument performance using total ion current (TIC).

Features

1. Total Ion Current

   • Total Ion Chromatogram

   • Statistical Analysis

     • Principal Component Analysis

       • Mass calibration, analyte and wash region

     • Time series analysis

       • Prewash region = Mass calibration region + Analyte region

     • Violin/Box plot analysis

       • Mass calibration
       • Analyte

2. Base Peak Intensity

   • Base Peak Chromatogram

3. Extracted Ion Current (Targeted)

   • Mass calibration references, internal standards, endogenous analytes and products

     • Chromatogram

     • Statistical Analysis

       • Time series
       • Mass accuracy

Installation

install.packages("remotes")
remotes::install_github("vmalnathnambiar/ticq")

Usage

The package primarily works in relation with ExfilMS, specifically for its functionality in extracting and filtering MS spectral data into a standardised JSON format.

ticq::renderTICQ(inputPath = "/path/to/input/directory/or/file.json", ...)

Limitations

Citations

If you use TICQ in your work, please cite it using the following:

Nambiar, V., & Nambiar, S. (2024). TICQ: Total Ion Current Quality Assessment of Mass Spectrometry Spectral Data (Version 0.0.0) [Computer software]. https://doi.org/10.5281/zenodo

License

Please refer to our license information here.