Version:	1.9.3
Date:	2024-10-02
Title:	Reads Mass Spectrometry Data in Bruker *flex Format
Depends:	R (≥ 3.3.0)
Suggests:	testthat
Description:	Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.
License:	GPL (≥ 3)
URL:	https://strimmerlab.github.io/software/maldiquant/, https://github.com/sgibb/readBrukerFlexData/
BugReports:	https://github.com/sgibb/readBrukerFlexData/issues/
LazyLoad:	yes
RoxygenNote:	7.3.1
Encoding:	UTF-8
NeedsCompilation:	no
Packaged:	2024-10-02 21:01:19 UTC; sebastian
Author:	Sebastian Gibb [aut, cre], Samuel Granjeaud [ctb], Alan Race [ctb]
Maintainer:	Sebastian Gibb <mail@sebastiangibb.de>
Repository:	CRAN
Date/Publication:	2024-10-02 21:20:02 UTC

The readBrukerFlexData Package

Description

The readBrukerFlexData package reads data files acquired by MALDI-TOF MS on Bruker Daltonics machines of the *flex series. (autoflex, microflex, ultraflex).
The package was developed without any knowledge nor even support by Bruker Daltonics.

All trademarks are owned by or licensed to Bruker Daltonics.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

https://github.com/sgibb/readBrukerFlexData

See Also

Useful links:

• https://strimmerlab.github.io/software/maldiquant/

• https://github.com/sgibb/readBrukerFlexData/

• Report bugs at https://github.com/sgibb/readBrukerFlexData/issues/

Change precision.

Description

This function converts double values to double values in a given precision (only correctly working for cut a higher precision to a lower one; e.g. IEEE 754 double precision to IEEE 754 single precision)

Usage

.changePrecision(x, size)

Arguments

Value

double.

See Also

.double2singlePrecision,

Cubic calibration

Description

Only basic support (not 100% identical results) for Bruker Daltonics' cubic calibration (encoded in '"##$NTBCal"' as '"V1.0CTOF2CalibrationConstants"'). This is an internal function and should normally not used by the user.

Usage

.ctof2calibration(tof, d)

Arguments

Value

double, mz values.

Note

Bruker Daltonics doesn't explain how the cubic calibration works. All formula are results of “trial and error”. That is why mass calculated by .ctof2calibration differs little from original mass. See also https://github.com/sgibb/readBrukerFlexData/issues/3.

Author(s)

Alan Race, Samuel Granjeaud, Sebastian Gibb

See Also

https://github.com/sgibb/readBrukerFlexData/issues/3

Converts double to single precision.

Description

This function simulates the conversion of floating point numbers from double precision (64bit, R: double(), C: double) to single precision (32bit, R: none, C: float). It follows IEEE 754 standard.

Usage

.double2singlePrecision(x)

Arguments

Details

The same could be done in C by using casts:

double precision32(double value) {
  float x=value;
  return (double)x;
}

Value

double (in single precision).

References

IEEE 754 standard: https://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=30711&filter=AND(p_Publication_Number:2355)

See Also

.changePrecision, .hpc

Examples

## load library
library("readBrukerFlexData")

## show more details
oldDigits <- options()$digits
options(digits=22)

## a test number
num <- 1/3

num
readBrukerFlexData:::.double2singlePrecision(num)

## reset digits option
options(digits=oldDigits)

Extracts High Precision Calibration coefficients.

Description

This is a helper function to extract coefficients and constants from metaData$hpcStr.

Usage

.extractHPCConstants(hpcStr)

Arguments

hpcStr <- "V1.0CHPCData  Order 10 vCoeff V1.0VectorDouble 11
           -0.48579224953906053 0.0009361303203700988
           -6.92711401708155e-008 -1.0992953299897006e-009
           1.1718229914003113e-012 -5.392578762547374e-016
           9.0176664604755316e-020 1.9704001597871883e-023
           -1.1794161284667635e-026 2.0351573912658823e-030
           -1.2617853301428769e-034
           c2 -0.046701600316874939
           c0 237.64781433281422
           minMass 736.50266799999997
           maxMass 3698.6377320000001 bUse 1 endCHPCData"

Value

a list:

• hpcConstants$coefficients: double, vector of coefficents

• hpcConstants$calibrationConstant0: c0

• hpcConstants$calibrationConstant2: c2

See Also

.hpc

Extracts values from acqu file.

Description

This function is a helper function to extract double values from acqu file.

Usage

.grepAcquDoubleValue(patternStr, srcStr)

Arguments

Value

double vector of the value given in patternStr

See Also

.grepAcquValue, .readAcquFile

Extracts values from acqu file.

Description

This function is a helper function to extract values from acqu file.

Usage

.grepAcquValue(patternStr, srcStr)

Arguments

Value

character vector of the value given in patternStr

See Also

.grepAcquDoubleValue, .readAcquFile

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

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
https://pubmed.ncbi.nlm.nih.gov/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
https://pubmed.ncbi.nlm.nih.gov/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!
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)

Reads an acqu file.

Description

This function reads constants, calibrations values and a lot of more from acqu files.

Usage

.readAcquFile(fidFile, verbose = FALSE)

Arguments

Value

a list with metadata

See Also

readBrukerFlexFile,

Reads binary fid file.

Description

This function reads a binary fid file. A fid file contains intensities for all measured time points.

Usage

.readFidFile(fidFile, nIntensities, endian = "little")

Arguments

Value

A vector of intensity values.

See Also

.readAcquFile, readBrukerFlexFile

Creates sample name.

Description

This function guesses the name of current spot from filename.

Usage

.sampleName(fidFile)

Arguments

Value

character, sample name: e.g ‘Pankreas_HB_L_061019_A10’

Note

WARNING: if the 4th upper directory hasn't an unique name you will get equal names for your spot list

e.g. the following will create a list with 4 elements but only 2 unique spot names (2-100kDa:0_A1 and 2-100kDa:0_B1)
./Run1/2-100kDa/0_A1/1/1SLin/fid
./Run1/2-100kDa/0_B1/1/1SLin/fid
./Run2/2-100kDa/0_A1/1/1SLin/fid
./Run2/2-100kDa/0_B1/1/1SLin/fid

See Also

.readAcquFile, readBrukerFlexFile

Calculates mass from time-of-flight values.

Description

This function calculates mass from time of flight values based on the following article: Titulaer, M. K. and Siccama, I. and Dekker, J. L. and van Rijswijk, A. L. and Heeren R. M. and Sillevis Smitt, P. A. and Luider, T. M. (2006)
“A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls”, BMC Bioinformatics, 7: 403 https://pubmed.ncbi.nlm.nih.gov/16953879/

Usage

.tof2mass(tof, c1, c2, c3)

Arguments

Details

Arguments are imported from metadata (acqu-file).

Value

double, calculated mass

References

Titulaer, M. K. and Siccama, I. and Dekker, J. L. and van Rijswijk, A. L. and Heeren R. M. and Sillevis Smitt, P. A. and Luider, T. M. (2006)
“A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls”, BMC Bioinformatics, 7: 403 https://pubmed.ncbi.nlm.nih.gov/16953879/

Mass spectrum generated by Bruker Daltonics CompassXport

Description

This dataset was generated by Bruker Daltonics CompassXport and imported by readMzXmlFile to R. It is only needed for comparison between Bruker Daltonics' HPC and .hpc.

Format

A list containing a mass and an intensity vector.

Source

Examples/hpc/mzXML/hpc.mzXML

See Also

.hpc, readMzXmlFile

Removed functions in package readBrukerFlexData

Description

These functions are defunct and no longer available.

Details

mqReadBrukerFlex:

use importBrukerFlex instead.

Reads recursively mass spectrometry data in Bruker Daltonics XMASS format.

Description

This function leads recursively all mass spectrometry data in Bruker Daltonics XMASS format in a specified directory.

Usage

readBrukerFlexDir(
  brukerFlexDir,
  removeCalibrationScans = TRUE,
  removeMetaData = FALSE,
  useHpc = TRUE,
  useSpectraNames = TRUE,
  filterZeroIntensities = FALSE,
  verbose = FALSE
)

Arguments

Details

See readBrukerFlexFile.

Value

A list of spectra.

• [[1]]$spectrum$mass: A vector of calculated mass.

• [[1]]$spectrum$intensity: A vector of intensity values.

• [[1]]$metaData: A list of metaData depending on read spectrum.

See Also

importBrukerFlex, readBrukerFlexFile, .hpc

Examples

## load library
library("readBrukerFlexData")

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

## read example spectra
spec <- readBrukerFlexDir(file.path(exampleDirectory,
  "2010_05_19_Gibb_C8_A1"))

## plot spectra
plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n")

l <- length(spec)
legendStr <- character(l)
for (i in seq(along=spec)) {
  lines(spec[[i]]$spectrum$mass, spec[[i]]$spectrum$intensity, type="l",
        col=rainbow(l)[i])
  legendStr[i] <- spec[[i]]$metaData$fullName
}

## draw legend
legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1)

Reads mass spectrometry data in Bruker Daltonics XMASS format.

Description

This function reads mass spectrometry data in Bruker Daltonics XMASS format used by Bruker Daltonics mass spectrometer of *flex series (autoflex, microflex, ultraflex).

Usage

readBrukerFlexFile(
  fidFile,
  removeMetaData = FALSE,
  useHpc = TRUE,
  filterZeroIntensities = FALSE,
  keepNegativeIntensities = FALSE,
  verbose = FALSE
)

Arguments

Details

readBrukerFlexFile has to import the following data to calculating mass from acqu file:

If High Precision Calibration (HPC) is used, readBrukerFlexFile needs:

readBrukerFlexFile tries also to import [optional]:

import from file path:

filterZeroIntensities: Change default value is not recommended! If TRUE all intensities equal zero are removed. This parameter exists only to be compatible to Bruker Daltonics CompassXport's mzXML export function. For details see: ‘Release Notes for CompassXport 3.0.3’, cap. 6 ‘Filtering of Zero Intensities’: “Bruker Daltonics' Acquisition Software will compress Analysis raw data. To save on operation time and to keep export file sizes small, CompassXport 3.0.3 will filter out zero (0.0) intensities when exporting to mzXML or mzData ...”

keepNegativeIntensities: Change default value is not recommended! If TRUE negative intensity values are not replaced by zero. This parameter exists only to be compatible to Bruker Daltonics CompassXport.

Value

A list of spectra and metadata.

• spectrum$mass: A vector of calculated mass.

• spectrum$tof: A vector of time-of-flight data.

• spectrum$intensity: A vector of intensity values.

• metaData: A list of metaData depending on read spectrum.

See Also

https://github.com/sgibb/readBrukerFlexData/wiki, importBrukerFlex, readBrukerFlexDir, .hpc

Examples

## load library
library("readBrukerFlexData")

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

## read example spectrum
spec <- readBrukerFlexFile(file.path(exampleDirectory,
  "2010_05_19_Gibb_C8_A1/0_A1/1/1SLin/fid"))

## print metaData
print(spec$metaData)

## plot spectrum
plot(spec$spectrum$mass, spec$spectrum$intensity, type="l", col="red")