peak2list {IDSL.MXP}

Peak to List (The main function)

Description

This function returns a list of two data objects required for the mass spectrometry data processing.

Usage

peak2list(path, MSfileName = "")

Arguments

path

address of the mass spectrometry file

MSfileName

name of the mass spectrometry file with .mzML or .mzXML extensions

Value

scanTable

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.

spectraList

a list of matrices of m/z and intensity values for each chromatogram scan

Note

‘retentionTime' column in the 'scanTable’ object is presented in minute.

See Also

https://colab.research.google.com/drive/1gXwwuI1zzDHykKfodLSQQt5rwTuFEMpD

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)
p2l <- peak2list(path = temp_wd, MSfileName = "003.mzML")