readBrukerFlexData (version 1.2.3)

.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

vector of doubles. 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

vector of doubles. Coefficients needed by the HPC algorithm.

Value

• A vector of HPC corrected mass (double).

Details

Bruker Daltonics' don't explain how HPC works. All formula a 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' flex-series you can find an article about HPC principles: Johan Gobom, Martin Mueller, Volker Egelhofer, Dorothea Theiss, Hans Lehrach, and Eckhard Nordhoff A Calibration Method That Simplifies and Improves Accurate Determination of Peptide Molecular mass by MALDI-TOF MS Anal Chem. 2002 Aug 1; 74(15): 3915-23 http://www.ncbi.nlm.nih.gov/pubmed/12175185

References

Johan Gobom, Martin Mueller, Volker Egelhofer, Dorothea Theiss, Hans Lehrach, and Eckhard Nordhoff A Calibration Method That Simplifies and Improves Accurate Determination of Peptide Molecular mass by MALDI-TOF MS Anal Chem. 2002 Aug 1; 74(15): 3915-23 http://www.ncbi.nlm.nih.gov/pubmed/12175185

See Also

readBrukerFlexDir, readBrukerFlexFile, .double2singlePrecision

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!
spec <- readBrukerFlexFile(file.path(exampleDirectory, 
    "hpc/fid/0_A20/1/1SRef/fid"), filterZeroIntensities=TRUE);

## plot spectrum 
plot(spec$metaData$backup$mass, spec$spectrum$intensity, type="l", col="red", 
     xlim=c(1296, 1300));
lines(spec$spectrum$mass, spec$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)
spec$metaData$backup$mass32 <-
    readBrukerFlexData:::.double2singlePrecision(spec$metaData$backup$mass);
spec$spectrum$mass32 <- readBrukerFlexData:::.double2singlePrecision(spec$spectrum$mass);

## calculate deviance
d <- spec$metaData$backup$mass32-cpSpecHpcMzXml$spectrum$mass;
dHPC <- spec$spectrum$mass32-cpSpecHpcMzXml$spectrum$mass;

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

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