correctPrecursorMz: Precursor m/z correction of xcmsRaw object imported from mzML...

In ohgane/ShotgunLipidomicsR: Utility Functions for Analysis/Visualization of ShotgunLipidomics Data.

Description

This function is a kind of a bug fix for mzML (generated from ThermoRAW by msConvert) data acquired on LTQ-Orbitrap XL, with monoisotopic selection OFF under DDA settings. The setting results in the precursor mz entry in the mzML to be "monoisotopic mass" (even though "monoisotopic selection" is disabled). Therefore real precursor mz values are not read from the mzML file into xcmsRaw object. As the real precursor m/z values are still present in the mzML file (though only to 2 decimals), this function extract the real precursor m/z and pick peak near the m/z value.

Usage

correctPrecursorMz(xraw, path, mzabs = 0.05)

Arguments

xraw	An xcmsRaw object.
path	A path to the original mzML file.
mzabs	Window size to search real precursor m/z value (default 0.05).

Value

xcmsRaw object with corrected precursor m/z values

ohgane/ShotgunLipidomicsR documentation built on May 24, 2019, 11:55 a.m.