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")).
Maintainer: Jaehyun Joo jaehyunjoo@outlook.com
Authors:
Blanca Himes
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