readBrukerFlexFile: Reads mass spectrometry data in Bruker Daltonics' XMASS format.

Description

Reads mass spectrometry data in Bruker Daltonics' XMASS format used by Bruker Daltonics' mass spectrometer of *flex series.

Usage

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

Arguments

fidFile

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 delete after calculation.

useHpc

logical. Should Bruker Daltonics' High Precision Calibration be used if available? (see also: .hpc)

verbose

logical. Print verbose messages?

Value

A list of spectra and metadata.
spectrum$massA vector of calculated mass.
spectrum$tofA vector of time-of-flight data.
spectrum$intensityA vector of intensity values.
metaDataA list of metaData depending on read spectrum.

Details

readBrukerFlexFile has to import the following data to calculating mass from acqu file: lll{ acqu-value becomes metaData description $TD metaData$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: lll{ 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]: lll{ 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 $Masserr metaData$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 measurement with this target $TgSer metaData$target$serialNumber target serial number $TgTyp metaData$target$typeNumber target type number }

import from file path: lll{ value becomes metaData description full current path to fid file metaData$file path on local machine sample name metaData$sampleName - }

Examples

Run this code

## 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");