Package 'readBrukerFlexData'

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 [email protected]

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/

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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

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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

brukerFlexDir	character, path to directory which should be read recursively.
removeCalibrationScans	logical, if TRUE all scans in directories called [Cc]alibration will be ignored.
removeMetaData	logical, to calculate mass data a lot of meta data are needed. To save memory they could be deleted after calculation.
useHpc	logical, should Bruker Daltonics' High Precision Calibration be used if available? (see also: .hpc)
useSpectraNames	logical, if TRUE all list elements get an unique name from metaData otherwise file path is used. (If ‘removeMetaData’ is TRUE ‘useSpectraNames’ has no effect.)
filterZeroIntensities	logical, don't change it. If TRUE all intensities equal 0.0 are removed. (see also: readBrukerFlexFile)
verbose	logical, print verbose messages?

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)

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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

fidFile	character, path to fid file which should be read.
removeMetaData	logical, to calculate mass data a lot of meta data are needed. To save memory they could be deleted after calculation.
useHpc	logical, should Bruker Daltonics' High Precision Calibration be used if available? (see also: .hpc)
filterZeroIntensities	logical, don't change it. If TRUE all intensities equal 0.0 are removed. (see also: ‘Details’ section)
keepNegativeIntensities	logical, don't change it. If FALSE all intensities less than zero are replaced by zero. (see also: ‘Details’ section)
verbose	logical, print verbose messages?

Details

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

acqu-value	becomes metaData	description
$BYTORDA	metaData$byteOrder	endianness of fid file
$TD	metaData$number	total number of measured time periods
$DELAY	metaData$timeDelay	first measured intensity after metaData$timeDelay ns
$DW	metaData$timeDelta	ns between measured time periods
$ML1	metaData$calibrationConstants[1]	mass calibration constant
$ML2	metaData$calibrationConstants[2]	mass calibration constant
$ML3	metaData$calibrationConstants[3]	mass calibration constant

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

acqu-value	becomes metaData	description
$HPClBHi	metaData$hpc$limits[“maxMass”]	upper mass threshold
$HPClBLo	metaData$hpc$limits[“minMass”]	lower mass threshold
$HPClOrd	metaData$hpc$order	polynomial order
$HPClUse	metaData$hpc$use	maybe using of HPC? (seems to be always “yes” in our test data)
$HPCStr	metaData$hpc$coefficients	polynomial coefficients in a string

readBrukerFlexFile tries also to import [optional]:

acqu-value	becomes metaData	description
DATATYPE	metaData$dataType	e.g CONTINUOUS MASS SPECTRUM
SPECTROMETER/DATASYSTEM	metaData$dataSystem	e.g. Bruker Flex Series
.SPECTROMETER TYPE	metaData$spectrometerType	e.g. TOF
.INLET	metaData$inlet	DIRECT
.IONIZATION MODE	metaData$ionizationMode	e.g. LD+
$DATE	metaData$date	same as $AQ_DATE but often only "0"
$ACQMETH	metaData$acquisitionMethod	path to method file
$AQ_DATE	metaData$acquisitionDate	acquisition date
$AQ_mod	metaData$acquisitionMode	acquisition mode
$AQOP_m	metaData$acquisitionOperatorMode, metaData$tofMode	LINEAR / REFLECTOR
$ATTEN	metaData$laserAttenuation	laser beam attenuation
$CMT[1:4]	metaData$comments	comments
$DEFLON	metaData$deflection	deflection ON/OFF
$DIGTYP	metaData$digitizerType	type of digitizer
$DPCAL1	metaData$deflectionPulserCal1	deflection pulser cal 1
$DPMASS	metaData$deflectionPulserMass	deflection pulser mass
$FCVer	metaData$flexControlVersion	Version of Bruker Daltonics FlexControl software
$ID_raw	metaData$id	spectrum id
$INSTRUM	metaData$instrument	e.g. AUTOFLEX
$InstrID	metaData$instrumentId	ID of mass spectrometer
$InstTyp	metaData$instrumentType	instrument type
$Lift1	metaData$lift[1]	LIFT constant?
$Lift2	metaData$lift[2]	LIFT constant?
$Masserr	metaData$massError	initial mass error in ppm
$NoSHOTS	metaData$laserShots	number of applied laser shots
$PATCHNO	metaData$patch	sample postion on target
$PATH	metaData$path	original file path (on Bruker *flex series controller PC)
$REPHZ	metaData$laserRepetition	laser repetition rate in Hz
$SPOTNO	metaData$spot	same as $PATCHNO (in older files often empty, that's why readBrukerFlexFile uses $PATHNO instead)
$SPType	metaData$spectrumType	e.g. TOF
$TgIDS	metaData$target$id	target ids
$TgCount	metaData$target$count	number of measurements with this target
$TgSer	metaData$target$serialNumber	target serial number
$TgTyp	metaData$target$typeNumber	target type number
$TLift	metaData$tlift	LIFT constant?

import from file path:

value	becomes metaData	description
full current path to fid file	metaData$file	path on local machine
sample name	metaData$sampleName	-

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")

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