IPPD-package: Peak pattern deconvolution for Protein Mass Spectrometry by
non-negative ls/lad template matching
Description
The package provides functionality to extract isotopic peak
patterns from raw mass spectra. This is done by fitting a large set of
template basis functions to the raw spectrum using nonnegative least
squares (ls) or nonnegative least absolute deviation (lad). Ideally, the nonnegativity constraint in combination with
nonnegativity of the template basis functions effects
that templates not matching the data are assigned an extremely low
weight such that one can easily identify isotopic patterns present and
not present in the spectrum. In practice, the templates only
approximate the peak patterns, where the quality the approximation
crucially depends on how well the shapes of the templates fit the
isotopic patterns contained in a spectrum. For this reason, the
package offers the flexible function fitModelParameters which
tries to estimate model parameters, e.g. the width of a
Gaussian bump, in a way tailored to the peak shapes in the data. As
second peak model in addition to the standard Gaussian, the package
offers full support for the Exponential Modified Gaussian.
The function getPeaklist predicts the set of isotopic peak
patterns present in the spectrum in a fully automatic, yet
customizable way. The main benefits of our approach are that
- Overlapping peak patterns can be resolved.
- The complete spectrum can be processed as a whole or in
large sections by exploiting the sparse nature of the problem.
- The set of parameters in getPeaklist are easy to
interpret and require only very basic knowledge of statistics.
- A theoretically well-founded post-processing procedure is used.
- The result can be analyzed visually in a detailed way using the function
visualize.
|
Package: |
| IPPD |
|
Type: |
| Package |
|
Version: |
| 1.3.1 |
|
Date: |
| 2012-01-17 |
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License: |
| GPL (version 2 or later) |