acqu file

The acqu and acqus file (they are identical) store information about the experiment. Also you find the coefficents to calculate the TOF and the corresponding mass values.

The acqu file contains key-value-pairs divided by an =. Each key starts with two #:

##TITLE=  XMASS Parameter file
##JCAMPDX=  5.0
##DATATYPE=  CONTINUOUS MASS SPECTRUM
##ORIGIN=  XMASS, Bruker-Daltonics (USA) and Bruker-Daltonik (GER)
##OWNER=  TOF User
##SPECTROMETER/DATASYSTEM=  Bruker Flex Series
##.SPECTROMETER TYPE=  TOF
##.INLET=  DIRECT
##.IONIZATION MODE=  LD+
##$ACQMID= 0 
##$ACQVSMA= 3 
##$ACQVSMI= 0 
##$ADC= 1

TOF calculation

##$TD: total number of measured time periods
##$DELAY: first measured intensity after ##$DELAY ns (t_0)
##$DW: ns between each measurement point

To calculate the different time points: ##$DELAY + 0:(##$TD - 1) * ##$DW

tof <- as.double(metaData$timeDelay + ((0:(metaData$number-1)) * metaData$timeDelta))

mass calculation

##$ML1 mass calibration constant 1
##$ML2 mass calibration constant 2
##$ML3 mass calibration constant 3

Here we use the equation described in Titulaer et al 2006; see implementation: https://github.com/sgibb/readBrukerFlexData/blob/master/R/tof2mass-functions.R

HPC mass calculation

Bruker Daltonics doesn't explain how their High Precision Calibration works. All formula are results of trial and error and partly based on Gobom et al 2002. HPC is a high order polynomial calibration (c0 + c1*mass + c2*mass^2 + ... + cn*mass^n). In the acqu file you find the following string, e.g.:

##$HPCStr= < V1.0CHPCData  Order 10 vCoeff V1.0VectorDouble 11 -0.30899977070432588 0.00012359234583847467 1.493619815861809e-006 -2.7525708852997263e-009 2.2224914282887503e-012 -9.267322574910882e-016 1.4960981457711781e-019 3.0715708656370546e-023 -1.8530337885161092e-026 3.203442186133685e-030 -1.9959759254400677e-034  c2 -0.048940611526270571 c0 225.86975630715625 minMass 736.50266799999997 maxMass 3814.7214599999998 bUse 1 endCHPCData >

The support for HPC isn't fully compatible yet. It seems that the calibration is only defined between minMass and maxMass. Please see the implementation for details: https://github.com/sgibb/readBrukerFlexData/blob/master/R/hpc-functions.R

The meaning of c0 (##$Hpcgc0) and c2 (##$Hpcgc2) is unknown.

LIFT values

##$Lift1 unknown
##$Lift2 unknown
##$TLift unknown

general information

##$BYTORDA the endianness of fid file (0: little, 1: big)
##$AQ_DATE acquisition date
##$DATE same as ##$AQ_DATE but often only 0
##$AQ_mod acquisition mode (0 = qf; 1 = qsim; 2 = qseq)
##$AQOP_m acquisition operator mode (0 = LINEAR; 1 = REFLECTOR)
##$ATTEN laser beam attenuation
##$CMT1 .. ##$CMT4 comments
##$DEFLON deflection ON/OFF (yes/no)
##$DIGTYP type of digitizer (0 = unknown; 1 = Lecroy LSA1000; 2 = Acqiris DP105; 3 = Acqiris DP110; 4 = Acqiris DP211; 5 = Acqiris DP240; 6 = Acqiris AP200; 7 = Acqiris AP240; 8 = Acqiris DC440; 9 = Acqiris DC282; 10 = Acqiris Unknown subtype; 11 = Gage; 12 = Simulator; 13 = Lecroy WaveRunner; 14 = Acqiris U1084A; 15 = NI 5154; 16 = LeCroy LSA2000; 17 = Acqiris DP1400; 18 = NI 5155; 19 = Bruker BD0G5)
##$DPMASS deflection pulser mass
##$FCVer Version of Bruker Daltonics FlexControl software
##$ID_raw spectrum id
##$INSTRUM instrument/device e.g. AUTOFLEX
##$InstrID ID of mass spectrometer
##$InstTyp instrument type (0 = autoflex; 1 = ultraflex; 2 = ultraflexTOF/TOF; 3 = reflex; 4 = biflex; 5 = omniflex; 6 = genoflex; 7 = massarray; 8 = autoflexTOF/TOF; 9 = microflex; 10 = MT10)
##$Masserr initial mass error in ppm
##$NoSHOTS number of applied laser shots
##$PATCHNO sample postion on target
##$PATH original file path (on Bruker *flex series controller PC)
##$REPHZ laser repetition rate in Hz
##$SPOTNO same as ##$PATCHNO (in older files often empty)
##$SPType spectrum type (0 = TOF; 1 = PSD; 2 = LIFT; 3 = PSDSegment)
##$TgIDS target ids
##$TgCount number of measurements with this target
##$TgSer target serial number
##$TgTyp target type number

See also: https://github.com/sgibb/readBrukerFlexData/blob/master/R/readAcquFile-functions.R

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