tofListMetaData {WMBrukerParser}R Documentation

Parsed TOF-MS Meta-Data

Description

tofListMetaData is a data.frame containing string values for experimental meta-data, with rows and columns addressable by spectrumName and attributeName, respectively.

Details

Meta-data can also be addressed using spectrum and attribute indices. This option should be used with caution since data and meta-data can be reordered independently during signal processing or statistical analysis.

Values can be updated if desired when tofListMetaData includes NAs due to missing optional parameter files.

Required meta-data attributes are parsed from required files.

Meta-data attributeNames include:

acquisitionInfo.arrayBarcode - Target (Bruker plate) identifier string, includes target type and target serial number - Required
acquisitionInfo.ionPolarity - “positive” or “negative” - Required
acquisitionInfo.refId - Spectrum identifier, used for spectrum vector names in tofList and rows names in tofListMetaData (generated by concatenating strings: sampleInfo.sampleName, “_ ”, and replicateNumber - Optional
acquisitionInfo.sourceFile - File name (with path) containing binary mass spectrum data, (from directory structure) - Automatic
acquisitionInfo.spotIndex - Spot index on MALDI plate - Automatic
acquisitionInfo.spotName - Spot name on MALDI plate - Automatic
adcGain.high - Digitizer gain factor - Optional
adcGain.low - Linear detector voltage - Optional
array.affinityType - Capture agent used for purification of biofluid samples - Optional
deflector.mode - 1 = linear, 2 = quadratic - Optional
experiment.id - Same as acquisitionInfo.refId - Optional
instrument.instrumentType - “Ultraflex Series” (hard coded) - Automatic
instrument.instrumentVendor - Name of instrument vendor - Required
instrument.serial - Instrument serial number - Required
instrumentSpecificSettings.adcBandwidth - Digitizer bandwith limit - Optional
instrumentSpecificSettings.adcOffset - Digitizer offset, depends on spectrum type and gain factor - Optional
instrumentSpecificSettings.adcScale - Digitizer sensitivity, depends on gain factor - Optional
instrumentSpecificSettings.detectorBaseVoltage - Detector base voltage, depends on spectrum type - Optional
instrumentSpecificSettings.laserIntensityBaseRange - Minimum laser power - Optional
instrumentSpecificSettings.laserShots - Number of laser shots per spot - Required
instrumentSpecificSettings.timeZero - Intial time in counts (calculated) - Required
instrumentSpecificSettings.TOFmode - Spectrometer mode: LINEAR or REFLECTOR - Automatic
instrumentSpecificSettings.warmingShots - Number of warming laser shots - Optional
laserIntensity.units - % (hard coded) - Automatic
laserIntensity.value - Maximum laser power, percent of full scale - Optional
laserIntensityWarming.units - % (hard coded) - Automatic
laserIntensityWarming.value - Warming Laser power, percent of full scale - Optional
mass.units - “Da” (hard coded) - Automatic
mass.value - Low mass cut off for matrix suppression - Optional
massCalibration.calibrationSpectrumFile - Calibration folder name. (If unavailable “?” is assigned as default) - Optional
massCalibration.dateCalibrated - Calibration date - Required
massCalibration.equation - c1*((T0+(X-1)*Tdelta)/U)^2+c0*((T0+(X-1)*Tdelta)/U)+c2 (hard coded) - Automatic
massEnd.units - Mass units, “Da” (hard coded) - Automatic
massEnd.value - Highest mass in acquisition range - Optional
massStart.units - Mass units, “Da” (hard coded) - Automatic
massStart.value - Lowest mass in acquisition range - Optional
param.c0 - linear coefficient in calibration equation - Required
param.c1 - quadratic coefficient in calibration equation - Required
param.c2 - constant term in calibration equation - Required
param.Mode - Calibration mode: 1 = linear, 2 = quadratic - Optional
param.T0 - Digitizer delay in ns - Required
param.TDelta - Dwell time in ns - Required
param.U - Nanoseconds/milliseconds conversion factor, “1e6” (hard coded) - Automatic
replicateNumber - Index of occurrence of sampleInfo.sampleName - Automatic
sampleInfo.groupName - Clinical group sample is associated with, used for classification analysis - Optional
sampleInfo.sampleDescription - Additional sample description - Optional
sampleInfo.sampleName - Sample identifier (if missing, the directory name is used as the default value) - Optional
sampleInfo.sampleSource - Laboratory where data was acquired (user supplied input parameter: ParserParams.dataSource) - Required
software.version - version of XACQ software - Required
spottingInfo.spotProtocol - Laser movement patern during data acquisition - Optional
timeOfFlightData.dateCreated - Data file creation date (from date stamp on fid file) - Automatic
timeOfFlightData.domain - Data domain, “time” (hard coded) - Automatic
timeOfFlightData.encoding - Data encoding, “base64” (hard coded) - Automatic
timeOfFlightData.end - Number of data points in spectra - Required
timeOfFlightData.offset - Initial value for offset of spectra, will be updated during alignment procedure, “0.0” (Hard coded) - Automatic
timeOfFlightData.pairOrder - Order of measurement pairs for TOF data, e.g., time - intensity, “t-int” (hard coded) - Automatic
timeOfFlightData.scale - Initial value for linear scale coefficient for spectra, updated during alignment: “1.0” (hard coded) - Automatic
timeOfFlightData.start - Index for onset of data acquisition, hard coded: “1” - Automatic

See Also

WMBrukerParser, BrukerParser,ParserParams, ParseAndSave, tofList

Examples


## To access a value:

data(tofListMetaDataRun2)

sampleName <- tofListMetaData["Pool 8_1","sampleInfo.sampleName"];

## To update a value 

tofListMetaData[ "Pool 8_2", "sampleInfo.sampleDescription" ] <- "Pool";

## To update the tofListMetaData rownames (desirable if default 
## assignments were used due to missing sampleInfo.sampleNames):

newSpecNames<-list();
numSpec<-dim(tofListMetaData)[1];
for (i in 1:numSpec) { newSpecNames[i]<-paste("spec",i,sep="")};
row.names(tofListMetaData)<-newSpecNames;

[Package WMBrukerParser version 1.1 Index]