readMSdata: Read LC-HRMS measurement .mzXML data

Description

Initiates an MSlist object and reads LC-HRMS measurement data from .mzXML files.

Usage

readMSdata(filepath.mzXML, MSlevel=c(1), progbar=FALSE, minRT=FALSE, 
maxRT=FALSE, minmz=FALSE, maxmz=FALSE, ion_mode=FALSE)

Arguments

filepath.mzXML

Path to the .mzXML file to be read

MSlevel

numeric 1 (MS) or 2 (MS-MS)

progbar

Show a progress bar (TRUE or FALSE)? Might only work in Windows OS

minRT

Filter for measurements with retention time >= minRT. Otherwise set to FALSE.

maxRT

Filter for measurements with retention time

minmz

Filter for measurements with m/z >= minmz. Otherwise set to FALSE.

maxmz

Filter for measurements with m/z

ion_mode

"positive" or "negative" ionization. Otherwise set to FALSE, see details.

Value

State: MSlist[[1]]: tags the individual steps the MSlist has undergone.
Parameters: MSlist[[2]]: saves parameter settings.
Results: MSlist[[3]]: saves a result summary.
Scans: MSlist[[4]]: matrix with raw measurements (m/z, intensity, RT) and tags for partitions, EIC cluster and individual peaks.
Partition_Index: MSlist[[5]]: Index assigning partitions to sections in the raw measurment of MSlist[[4]]. Needed for fast (random) access during, e.g., plotting.
EIC_index: MSlist[[6]]: Index assigning EIC clusters to sections in the raw measurment of MSlist[[4]]. Required for fast access.
Peak_index: MSlist[[7]]: Index assigning picked peaks to sections in the raw measurment of MSlist[[4]]. Required for fast access.
Peaklist: MSlist[[8]]: Final peak list, cp. mzpick

Warning

Use plotMSlist to check your data in MSlist for consistency at an early stage before further processing.

Details

The return value, a so-called MSlist object, is a simple R list object that contains (a) the raw measurement data, (b) intermediate/final results of the peak picking procedure and (c) indices for random access, to be passed among functions. Peaks are nested in EIC clusters which in turn are nested in partitions which in turn are subsets of measurements; MSlist[[4]] is resorted accordingly during all peak picking steps.