Maximum measurement deviation (+/-) of m/z within an EIC, mzclust
ppm
dmzgap, given in ppm (TRUE) or as absolute value (FALSE)
drtgap
RT gap width for partitioning, mzpart
drtsmall
Peak definition - RT window of a peak; cp. minpeak argument
drtdens
Maximum length of EICs, mzclust
drtfill
RT gap length to be filled, mzpick
drttotal
Maximum RT length of a single peak, mzpick
minpeak
Peak definition - minimum number of measurements per peak to found in windows of drtsmall and dmzsmall, mzpick
recurs
Maximum number of peaks within one EIC, mzpick
weight
Weight for assigning measurements to a peak, mzpick
SB
Signal-to-base ratio, mzpick
SN
Signal-to-noise ratio, mzpick
minint
Minimum intensity of a peak, mzpick
maxint
Peaks above this intensity are alwas included, regardless of checks for SB or SN,mzpick
ended
Within the peak detection recursion set by argument recurs, how often can a peak detection fail, to end the recursion? mzpick
ion_mode
"positive" or "negative" ionization. Otherwise set to FALSE, see details.
progbar
Show a progress bar (TRUE or FALSE)? May only work under Windows OS.
Details
For further details on the parameter settings, please refer to the arguments of the underlying functions readMSdata,
mzagglom, mzclust and mzpick.
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 for peak picking.
Parameters
MSlist[[2]]: saves the parameter settings.
Results
MSlist[[3]]: saves the result summary values
Scans
MSlist[[4]]: matrix with raw measurements (m/z, intensity, RT) and tags for partitions, EIC cluster or individual peaks.
Partition_Index
MSlist[[5]]: Index assigning partitions to sections in the raw measurment of MSlist[[4]]. Required for fast (random) access, 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.