locate.peaks: Locate Peaks in a FT-ICR MS Spectrum

Description

Locates peaks in FT-ICR MS spectra assuming that the peaks are roughly parabolic on the log scale.

Usage

locate.peaks(peak.base, num.pts = 5, R2.thresh = 0.98,  oneside.min = 1, peak.method = c("parabola", "locmaxes"),  thresh = -Inf)

Arguments

peak.base

numeric matrix with two columns containing the masses and the transformed spectrum intensities

num.pts

minimum number of points needed to have a peak

R2.thresh

minimum $R^2$ needed to have a peak

oneside.min

minimum number of points needed on each side of the local maximum

peak.method

how to locate peaks

thresh

only local maxes that are larger than this will be checked to see if they are peaks

Value

Center_hat: estimated mass of peak
Max_hat: estimated intensity of peak
Width_hat: estimated width of peak

Details

If peak.method == "parabola", the algorithm works by locating local maxima in the spectrum, then seeing if any num.pts consecutive points with at least oneside.min point(s) on each side of the local maximum have a coefficient of determination ($R^2$) of at least R2.thresh when fitted with a quadratic. If, in addition, the coefficient of the squared term is negative, then this is declared a peak and the vertex of the corresponding parabola is located. The coordinates of the vertex give the components Center_hat and Max_hat in the return value. The Width_hat component is the negative reciprocal of the coefficient of the squared term.

If peak.method == "locmax", then the algorithm merely returns the set of local maxima larger than thresh, and the Width_hat component of the return value is NA.

References

Barkauskas, D.A. and D.M. Rocke. (2009a) “A general-purpose baseline estimation algorithm for spectroscopic data”. to appear in Analytica Chimica Acta. doi:10.1016/j.aca.2009.10.043

Barkauskas, D.A. et al. (2009b) “Analysis of MALDI FT-ICR mass spectrometry data: A time series approach”. Analytica Chimica Acta, 648:2, 207--214.