Learn R Programming

rtmsEcho (version 0.2.4)

Extract and Analyze EchoMS Data from Sciex Wiff Files

Description

Read raw and processed data from acoustic ejection mass spectrometry (AEMS) files produced by the Sciex EchoMS instrument. Includes functions to create interactive reader objects, extract raw intensity measurements, mass spectra, and fully-processed mass-transition intensity areas. Methods for data processing and analysis are described in Rimmer et al. (2025) . Supports both multiple reaction monitoring (MRM) and full-scan (neutral loss and precursor ion) data formats.

Copy Link

Version

Install

install.packages('rtmsEcho')

Version

0.2.4

License

GPL (>= 3)

Maintainer

Nathaniel Twarog

Last Published

January 14th, 2026

Functions in rtmsEcho (0.2.4)

measureEjections

Measure total ion chromatogram peaks to estimate ejection time
getWiffShots

List of Shot Names in a given Wiff File
processAllMRMAreas

Process an MRM file in total
getFullScanAreas

Get the total area for given masses for a particular well
getMRMAreas

Extract the peak areas for MRM mass transitions for a given well
getAllFullScanAreas

Get the total area for given masses for all wells
getAllTIC

Extract all total ion chromatograms from a Wiff file
getFullScanSpectrum

Extract a full mass spectrum for a given well
getFullScanData

Extract raw Wiff full scan data
exampleWiff

Example wiff reader object
getMRMChromatograms

Extract full chromatograms for each mass transition
getAllMRMAreas

Extract the peak areas for MRM mass transitions for all wells
getAllFullScanSpectra

Extract mass spectra for all wells
getTIC

Extract a total ion chromatogram (TIC) from a Wiff file
newWiffReader

Open a Sciex EchoMS wiff File for Reading
processAllFullScanAreas

Fully process a Full Scan Wiff and scan File