recalibrate.massvectorlist {mscalib}R Documentation

Precalibration

Description

Obtains the error and performs the calibration in one step.

Usage

## S3 method for class 'massvectorlist':
recalibrate(object,PQM=7,...)

Arguments

... further parameters.
PQM Peak Quality Measure. Indicates how well the wavelenght of the massvector was determined.
object massvectorlist.

Details

Precalibration method utilizes the knowledge that masses of peptides are in equidistant spaced clusters. The wavelength of the massesvector can be determined as described by Wool. The comparision of the experimental wavelength with the theoretical one, makes possible to find an affine function that corrects the masses. Chemical noise in the spectra may hamper the determination of mass list frequency. The package provides a function to filter chemical noise.

Value

massvectorlist recalibrated massvectorlist.

Author(s)

Witold Wolski wolski@molgen.mpg.de

References

-
Wool A, Smilansky Z 2002. Precalibration of matrix-assisted laser desorption/ionization-time of flight spectra for peptide mass fingerprinting. Proteomics. 2(10):1365-73.
-
Wolski http://www.molgen.mpg.de/~wolski/mscalib

See Also

recalibrate.massvector,

Examples

 data(mvl)
 mvl<-mvl[1:100]
 pp <- recalibrate(mvl,PQM=8)
 compare(pp[[1]],mvl[[1]],error=1,ppm=FALSE)

[Package mscalib version 0.5.9 Index]