MALDIquant: monoisotopicPeaks-methods – R documentation

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monoisotopicPeaks-methods

Finds monoisotopic peaks in a MassPeaks object.

Description

This method looks for monoisotopic peaks in peak list data (represented by a MassPeaks objects).
It is based on the poisson model for isotopic patterns described in Breen et al 2000.

Usage

## S4 method for signature 'MassPeaks'
monoisotopicPeaks(object,
  minCor=0.95, tolerance=1e-4, distance=1.00235, size=3L:10L)
## S4 method for signature 'list'
monoisotopicPeaks(object, ...)

Arguments

`object`	`MassPeaks` object or a `list` of `MassPeaks` objects.
`minCor`	`double`, minimal correlation between the peak pattern generated by the model and the experimental peaks in the `MassPeaks` object to be recognized as isotopic pattern.
`tolerance`	`double`, maximal relative deviation of peaks position (mass) to be considered as isotopic distance ( `abs(((mass[i]+distance)-mass[i+1])/mass[i]) < tolerance`).
`distance`	`double`, distance between two consecutive peaks in an isotopic pattern (default value taken from Park et al 2008). Could contain more than one value, e.g. `distance=(1:3)^-1` to find isotopic patterns for multiple charged patterns (e.g. 1+, 2+, and 3+). Please note that the order matters here if there is a monoisotopic peak for charge state 1 and 3 it would be reported as charge 1 for `distance=(1:3)^-1` and as 3 for `distance=(3:1)^-1` respectively.
`size`	`double`, size (length) of isotopic pattern, longer patterns are prefered over shorter ones.
`...`	arguments to be passed to `monoisotopicPeaks,MassPeaks-method`. If `object` is a `list` `mc.cores` is also supported.

Value

Returns a MassPeaks object with monoisotopic peaks only.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

K. Park, J.Y. Yoon, S. Lee, E. Paek, H. Park, H.J. Jung, and S.W. Lee. 2008. Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data. Analytical Chemistry, 80: 7294-7303.

E.J. Breen, F.G. Hopwood, K.L. Williams, and M.R. Wilkins. 2000. Automatic poisson peak harvesting for high throughput protein identification. Electrophoresis 21: 2243-2251.

Examples

## load package
library("MALDIquant")

## create example peaks
p <- createMassPeaks(mass=995:1005,
                     intensity=c(100, 10, 30, 10, 40, # noise
                                 550, 330, 110, 10,   # isotopic pattern
                                 5, 15))              # more noise
m <- monoisotopicPeaks(p)
as.matrix(m)

## plot the peaks and mark the monoisotopic one
plot(p)
points(m, col=2, pch=4)

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12