mzpick: EIC peak picking

Description Usage Arguments Details Value imbecile Author(s) See Also

Description

Peak-picking within individual EIC cluster formed by mzclust without assuming a certain peak shape. Includes a baseline subtraction step.

Usage

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mzpick(MSlist, minpeak = 4, drtsmall = 20, drtfill = 10,  drttotal = 200, recurs = 4, 
weight = 2, SB = 3, SN=2, minint = 1E4, maxint = 1e+07, ended = 2, progbar = FALSE, 
from = FALSE, to = FALSE)

Arguments

MSlist

An MSlist returned by mzclust

minpeak

Peak definition - minimum number of measurements required within the RT window of drtsmall

drtsmall

Peak definition - RT window of a peak; cp. minpeak argument

drtfill

Maximum RT gap length to be filled, cp. details

drttotal

Peak definition - Maximum RT length of a single peak

recurs

Maximum number of peaks within one EIC, cp. details

weight

Weight for assigning measurements to a peak, cp. details

SB

Peak definition - signal-to-base ratio

SN

Peak definition - signal-to-noise ratio

minint

Peak definition - minimum intensity of a peak

maxint

Peaks above this intensity are always retained, regardless of other checks

ended

Within the peak detection recursion set by argument recurs, how often can a peak detection fail to end the recursion?

progbar

For debugging, ignore

from

For debugging, ignore

to

For debugging, ignore

Details

In a first step, RT gaps between measurements in an EIC not larger than drtfill are filled by linear interpolation. Subsequently, peaks are assigned over a number of recurs recursions not interrupted by more than ended times of failed peak detections.

At each recursion, the most intense EIC measurement not yet assigned to a peak is selected as peak apex and neighbouring unassigned measurements at lower and higher RT are evaluated for forming the peak. To this end, increases (lower RT) and decreases (higher RT) in intensity of consecutive measurements over a maximum RT width of drtdens are summed and penalized by a factor of weight for intensity reversions. The measurements with optimum values are then selected to define the start and end measurement of the peak.

Thereupon, the candidate peak is checked to (a) have at least minpeaks within a RT window of drtsmall, (b) be larger than the minimum peak intensity minint and (c) have a minimum SB ratio (the ratio between the most intense measurement and the mimimum intensity of the first or last peak measurement). Candidate peaks failing in any of the aspects (a) to (c) are discarded (adding to ended), unless they are higher in intensity than maxint.

Next, all measurements assigned to peaks are removed from the EIC and the resulting gaps linearly interpolated and smoothed by a moving window average to form a baseline. The latter is then subtracted from the assigned peaks.

In a last step, peaks are checked for their signal-to-noise SN ratio in relation to the baseline measurements (if present). Herein, SN is defined as the ratio between the most intense (baseline-corrected) peak measurement and the median of the difference between the non-peak measurements (if any) and the baseline.

Value

Returns the argument MSlist, with entries made:

Parameters

MSlist[[2]]: saves the parameter settings.

Scans

MSlist[[4]]: matrix with raw measurements and tags for picked peaks within EICs within partitions.

Peak_index

MSlist[[7]]: Index assigning picked peaks to sections in the raw measurment of MSlist[[4]]. Required for fast access.

Peaklist

MSlist[[8]]: matrix with picked peak characteristics, with columns: m/z (mean m/z of peak measurements), var_m/z (m/z variation of peak measurements), max_int (base-line corrected maximum intensity), sum_int (sum of all base-line corrected peak measurement intensities), RT (retention time at maximum intensity), minRT (start peak RT), maxRT (end peak RT), peak# (peak ID number), EIC# (EIC ID number) and Score (not yet implemented).

imbecile

ended must be smaller than recurs. minpeak and drtsmall should be congruent in both and mzclust and mzpick.

Author(s)

Martin Loos

See Also

plotMSlist writePeaklist


enviPick documentation built on May 1, 2019, 8:05 p.m.