plotTopMS2Peaks: Extract top MS2 ions from MS1 EIC interactively

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

Extract top MS2 ions from MS1 EIC interactively

Description

A Shiny app that displays extracted ion chromatograms from MS1 data. Click on a peak to select a retention time window, then extract the most intense MS2 ions from that window and overlay their chromatograms.

Usage

plotTopMS2Peaks(
  filepath,
  featlist,
  numTopIons = 10,
  diff = 0.01,
  rtWindow = 0.3
)

Arguments

filepath	character. Path to an mzML or mzXML file.
featlist	data.frame with columns: name, mz, ms_level.
numTopIons	integer. Number of most intense MS1 ions to extract. Default 10.
diff	numeric. Half-width of m/z extraction window (Da). Default 0.01.
rtWindow	numeric. Half-width of RT window (seconds) around clicked peak. Default 0.3.

Value

Opens an interactive Shiny app in the browser.

Examples

## Not run: 
targets <- data.frame(
  name = c("precursor1"),
  mz = c(500.1234),
  ms_level = c("ms1")
)
plotTopMS2Peaks("sample.mzML", targets, numTopIons = 5)

## End(Not run)

enviGCMS documentation built on Oct. 7, 2026, 5:07 p.m.