readBrukerFlexData: hpc – R documentation

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hpc

High Precision Calibration

Description

Only basic support (not 100% identical results) for Bruker Daltonics' HPC. HPC stands for High Precision Calibration.
This is an internal function and should normally not used by the user.

Usage

.hpc(mass, minMass, maxMass, hpcCoefficients)

Arguments

`mass`	`double`, mass calculated traditionally.
`minMass`	`double`, lower Threshold for HPC. HPC is only defined for a range of mass.
`maxMass`	`double`, upper Threshold for HPC. HPC is only defined for a range of mass.
`hpcCoefficients`	`doubles`, coefficients needed by the HPC algorithm (see also: `.extractHPCConstants`)

Details

Bruker Daltonics doesn't explain how HPC works. All formula are results of “trial and error”. That is why mass calculated by .hpc differs little from original HPC mass. (In example file 214 of 24860 mass are incorrect; deviations: min: 6.103515625e-05, max: 0.02935791015625.)
In the manual of mass spectrometry instruments of Bruker Daltonics machines the *flex series you can find an article about HPC principles:
Gobom, J. and Mueller, M. and Egelhofer V. and Theiss, D. and Lehrach, H. and Nordhoff, E. (2002)
“A Calibration Method That Simplifies and Improves Accurate Determination of Peptide Molecular mass by MALDI-TOF MS.”, Anal Chem 74: 3915-3923
http://www.ncbi.nlm.nih.gov/pubmed/12175185

Value

A vector of HPC corrected mass (double).

Note

Please note that .hpc is not correct! You have been warned.

References

Gobom, J. and Mueller, M. and Egelhofer V. and Theiss, D. and Lehrach, H. and Nordhoff, E. (2002)
“A Calibration Method That Simplifies and Improves Accurate Determination of Peptide Molecular mass by MALDI-TOF MS.”, Anal Chem 74: 3915-3923
http://www.ncbi.nlm.nih.gov/pubmed/12175185

Examples

## load library
library("readBrukerFlexData")

## get examples directory
exampleDirectory <- system.file("Examples", package="readBrukerFlexData")

## read example spectra
## please note: filterZeroIntensities=TRUE is used for compatibility reasons.
##              You should NOT use it!
noHpcSpec <- readBrukerFlexFile(file.path(exampleDirectory,
    "hpc/fid/0_A20/1/1SRef/fid"), filterZeroIntensities=TRUE, useHpc=FALSE)
hpcSpec <- readBrukerFlexFile(file.path(exampleDirectory,
    "hpc/fid/0_A20/1/1SRef/fid"), filterZeroIntensities=TRUE)

## plot spectrum
plot(noHpcSpec$spectrum$mass, noHpcSpec$spectrum$intensity, type="l",
     col="red", xlim=c(1296, 1300))
lines(hpcSpec$spectrum$mass, hpcSpec$spectrum$intensity, type="l",
      col="green", xlim=c(1296, 1300))
legend(x="topright", legend=c("no hpc", "hpc"), col=c("red", "green"), lwd=1)

## show difference between .hpc and original HPC
## load mzXML generated by Bruker Daltonics CompassXport 1.3.5
## you could do it like this:
#library("readMzXmlData")
#cpSpecHpcMzXml <- readMzXmlFile(file.path(exampleDirectory,
#  "hpc/mzXML/hpc.mzXML"))

## or easily use:
data(cpSpecHpcMzXml)

## reduce R double precision to single precision because our CompassXport 1.3.5
## supports only mzXML with precision=32 (only for compatibility reasons)
noHpcSpec$spectrum$mass32 <-
 readBrukerFlexData:::.double2singlePrecision(noHpcSpec$spectrum$mass)
hpcSpec$spectrum$mass32 <-
 readBrukerFlexData:::.double2singlePrecision(hpcSpec$spectrum$mass)

## calculate deviance
d <- noHpcSpec$spectrum$mass32-cpSpecHpcMzXml$spectrum$mass
dHPC <- hpcSpec$spectrum$mass32-cpSpecHpcMzXml$spectrum$mass

## a little summary
cat("without .hpc:\n",
    "not matching: ", length(cpSpecHpcMzXml$spectrum$mass[d!=0]), " of ",
    length(cpSpecHpcMzXml$spectrum$mass), "; range: ",
    range(abs(d[d!=0])), "\nwith .hpc:\n",
    "not matching: ", length(cpSpecHpcMzXml$spectrum$mass[dHPC!=0]), " of ",
    length(cpSpecHpcMzXml$spectrum$mass), "; range: ",
    range(abs(d[dHPC!=0])), "\n")

##
## doing things manually
##
hpcMass <- readBrukerFlexData:::.hpc(mass=noHpcSpec$spectrum$mass,
 minMass=noHpcSpec$metaData$hpc$limits["minMass"],
 maxMass=noHpcSpec$metaData$hpc$limits["maxMass"],
 hpcCoefficients=noHpcSpec$metaData$hpc$coefficients)

readBrukerFlexData

Reads Mass Spectrometry Data in Bruker *flex Format

v1.8.5

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre]

Initial release

2017-04-22

hpc