plotTopMS1Peaks: Extract top MS1 ions from MS2 EIC interactively

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

Extract top MS1 ions from MS2 EIC interactively

Description

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

Usage

plotTopMS1Peaks(
  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: 
frags <- data.frame(
  name = c("Br79", "Br81"),
  mz = c(78.9183, 80.9163),
  ms_level = c("ms2", "ms2")
)
plotTopMS1Peaks("sample.mzML", frags, numTopIons = 3)

## End(Not run)

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