getScanTable: getScanTable

In IDSL.MXP: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)

getScanTable

Description

This function creates a scanTable from chromatogram scans of the mass spectrometry data.

Usage

getScanTable(xmlData, msFormat)

Arguments

xmlData	A structured data of the mass spectrometry data created by the 'read_xml' function.
msFormat	format extension of the mass spectrometry file c("mzML", "mzXML")

Value

a dataframe of different scan properties including 'seqNum', 'msLevel', 'polarity', 'peaksCount', 'totIonCurrent', 'retentionTime', 'basePeakMZ', 'basePeakIntensity', 'collisionEnergy', 'lowMZ', 'highMZ', 'precursorScanNum', 'precursorMZ', 'precursorCharge', 'precursorIntensity', 'injectionTime', 'filterString', 'scanType', 'centroided', 'isolationWindowTargetMZ', 'isolationWindowLowerOffset', 'isolationWindowUpperOffset', 'scanWindowLowerLimit', and 'scanWindowUpperLimit'. 'scanType' is only provided for the mzXML data format.

Note

'retentionTime' column is presented in minute.

Examples

temp_wd <- tempdir()
temp_wd_zip <- paste0(temp_wd,"/idsl_ipa_test_files.zip")
download.file(paste0("https://github.com/idslme/IDSL.IPA/blob/main/",
"IPA_educational_files/idsl_ipa_test_files.zip?raw=true"),
destfile = temp_wd_zip, mode = "wb")
unzip(temp_wd_zip, exdir = temp_wd)
xmlData <- xml2::read_xml(paste0(path = temp_wd, "/", MSfile = "003.mzML"))
scanTable <- getScanTable(xmlData, msFormat = "mzML")

IDSL.MXP documentation built on March 31, 2023, 9:02 p.m.