| Title: | Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment |
| Version: | 1.0.2 |
| Description: | The goal of 'LCMSQA' is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a 'shiny' application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Depends: | R (≥ 4.0.0) |
| Imports: | bsplus, data.table, DT, ggplot2, methods, plotly, shiny, shinycssloaders, shinyjs, shinyWidgets |
| Suggests: | BiocManager, xcms, MSnbase, knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2024-01-12 06:36:45 UTC; jaehyun |
| Author: | Jaehyun Joo [aut, cre], Blanca Himes [aut] |
| Maintainer: | Jaehyun Joo <jaehyunjoo@outlook.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-01-12 11:20:05 UTC |
LC/MS Quality Assessment
Description
The 'LCMSQA' package is designed to assess the quality of liquid chromatography/mass spectrometry (LC/MS) experiment using a user-friendly web application built with the R package 'shiny'. It utilizes the R package 'xcms' workflow for data import, visualization, and quality check of LC/MS experiments.
The application consists of four main tabs:
Total Ion Chromatogram (and Base Peak Chromatogram)
Extracted Ion Chromatogram (XIC)
Mass Spectrum
Metabolic Feature Detection
Please check the vignette for the details (Run vignette("LCMSQA",
package = "LCMSQA")).
Details
The application needs the following inputs:
(required) mass-spectrometry data files of quality control (QC) samples in open formats: AIA/ANDI NetCDF, mzXML, mzData and mzML.
(optional) internal standard information in a CSV format with the columns:
compound: the name of compound
adduct: adduct type (e.g., [M+H]+)
mode: must be either "positive" or "negative"
mz: a known mass-to-charge ratio (m/z) value
In the application UI, a user can tune the following parameters:
Set m/z and retention time of interest
compound (or m/z) with a ppm tolerance
retention time in second (min, max)
Peak picking using the centWave method (see xcms::CentWaveParam)
ppm: the maximal tolerated m/z deviation in consecutive scans in ppm for the initial region of interest (ROI) definition
peak width: the expected approximate peak width in chromatographic space
signal/noise cut: the signal to noise ratio cutoff
m/z diff: the minimum difference in m/z dimension required for peaks with overlapping retention times
noise: a minimum intensity required for centroids to be considered in the first analysis step
prefilter (>= peaks, >= intensity): the prefilter step for the first analysis step (ROI detection)
Gaussian fit: whether or not a Gaussian should be fitted to each peak
m/z center: the function to calculate the m/z center of the chromatographic peaks
integration: whether or not peak limits are found through descent on the Mexican Hat filtered data
Peak grouping using the peak density method (see xcms::PeakDensityParam)
bandwidth: the bandwidth (standard deviation of the smoothing kernel) to be used
min fraction: the minimum fraction of samples in which the peaks has to be detected to define a peak group
bin size: the size of overlapping slices in m/z dimension
Author(s)
Maintainer: Jaehyun Joo jaehyunjoo@outlook.com
Authors:
Blanca Himes
Start LC/MS QA application
Description
Runs a 'shiny' application to check the quality of LC/MS experiment. The system's default web browser will be launched automatically after the app is started.
Usage
runQA()
Value
This function normally does not return; interrupt R to stop the application (usually by pressing Ctrl + C or ESC)
Examples
## Please check the package vignette for details on how to use the app
if (interactive()) {
runQA()
}