readMSdata: Read LC-HRMS measurement .mzXML data

In blosloos/enviPick: Peak Picking for High Resolution Mass Spectrometry Data

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 <= maxRT. Otherwise set to FALSE.
minmz	Filter for measurements with m/z >= minmz. Otherwise set to FALSE.
maxmz	Filter for measurements with m/z <= maxmz. Otherwise set to FALSE.
ion_mode	"positive" or "negative" ionization. Otherwise set to FALSE, see details.

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.

Setting minRT, maxRT, minmz or maxmz allows you to filter your .mzML data. On the one hand, this may be very useful if only being interested in certain ranges of an experiment. On the other hand, this allows you to upload subset data of an experiment too large to be loaded into R at once. ion_mode allows to filter scans of a specific polarity from .mzXML files, if not set to FALSE; useful for files acquired under polarity switching.

Value

MSlist

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.

Note

It is your responsibility to ensure your input files are centroided. If not, R may freeze and the peak picker will not return valid results.

Author(s)

Martin Loos

See Also

mzagglom

blosloos/enviPick documentation built on Feb. 13, 2023, 12:03 p.m.