metaMS (version 1.8.0)

FEMsettings: Example settings for metaMS

Description

Examples of settings needed for functions runLC and runGC: Synapt.RP, Synapt.NP, TSQXLS.GC and Orbitrap.RP. These four particular settings are fine-tuned for the analysis of LC-MS runs, both normal-phase and reverse-phase chromatography (Waters Synapt G1-Thermo Orbitrap)and GC-MS experiments (ThermoXLS TQQ).

Usage

data(FEMsettings)

Format

Four objects of class metaMSsettings.

See Also

findPeaks, annotate

Examples

## Not run: 
# ## The three sets of settings are created as follows:
# Synapt.NP <- metaMSsettings(protocolName = "Synapt.QTOF.NP",
#                             chrom = "LC",
#                             PeakPicking = list(
#                               method = "matchedFilter",
#                               step = 0.05,
#                               fwhm = 20,
#                               snthresh = 4,
#                               max = 50),
#                             Alignment = list(
#                               min.class.fraction = .3,
#                               min.class.size = 3,
#                               mzwid = 0.1,
#                               bws = c(130, 10),
#                               missingratio = 0.2,
#                               extraratio = 0.1,
#                               Retcor = list(
#                                 method = "linear",
#                                 family = "symmetric"),            
#                               fillPeaks = TRUE),
#                             CAMERA = list(
#                               perfwhm = 0.6,
#                               cor_eic_th = 0.7,
#                               ppm= 5))
# metaSetting(Synapt.NP, "match2DB") <- list(
#             rtdiff = 1.5,
#             rtval = .1,
#             mzdiff = 0.005,
#             ppm = 5,
#             minfeat = 2)
# metaSetting(Synapt.NP, "DBconstruction") <- list(
#             minfeat = 3,
#             rttol = .3,
#             mztol = .01)
# 
# ## For reverse-phase LC, settings are very similar: the only difference
# ## is in the alignment settings
# Synapt.RP <- Synapt.NP
# metaSetting(Synapt.RP, "protocolName") <- "Synapt.QTOF.RP"
# metaSetting(Synapt.RP, "Alignment") <- list(
#             min.class.fraction = .3,
#             min.class.size = 3,
#             mzwid = 0.1,
#             bws = c(30, 10),
#             missingratio = 0.2,
#             extraratio = 0.1,
#             Retcor = list(
#               method = "linear",
#               family = "symmetric"),           
#             fillPeaks = TRUE)
# 
# 
# ## For the orbitrap.RP
# Orbitrap.RP <- metaMSsettings(protocolName = "Orbitrap",
#                               chrom = "LC",
#                                PeakPicking = list(
#                                  method = "centWave",
#                                  ppm = 5,
#                                  prefilter = c(3,10000),
#                                  peakwidth = c(15,40)),
#                              Alignment = list(
#                                  bws = 30,
#                                  min.class.fraction = 0.3,
#                                  min.class.size = 3,
#                                  mzwid = 0.01,
#                                  Retcor = list(
#                                   method = "obiwarp",
#                                   profStep = 0.2),
#                                  fillPeaks = TRUE),
#                              CAMERA = list(
#                                  perfwhm = 0.6,
#                                  cor_eic_th = 0.7,
#                                  ppm = 5))
# metaSetting(Orbitrap.RP, "match2DB") <- list(
#             rtdiff = 1.5,
#             rtval = .1,
#             mzdiff = 0.005,
#             ppm = 5,
#             minfeat = 2)
# metaSetting(Orbitrap.RP, "DBconstruction") <- list(
#             minfeat = 3,
#             rttol = .3,
#             mztol = .01)
# 
# ## For the thermo TQ
# 
# TSQXLS.GC <- metaMSsettings("protocolName" = "TSQXLS.QQQ.GC",
#                             "chrom" = "GC",
#                             PeakPicking = list(
#                               method = "matchedFilter",
#                               step = 0.5,
#                               steps = 2,
#                               mzdiff = .5,
#                               fwhm = 5,
#                               snthresh = 2,
#                               max = 500),
#                            CAMERA = list(perfwhm = 1))
# metaSetting(TSQXLS.GC, "DBconstruction") <- list(
#             minintens = 0.0,
#             rttol = .1,
#             intensityMeasure = "maxo",
#             DBthreshold = .80, 
#             minfeat = 5)
# metaSetting(TSQXLS.GC, "match2DB") <- list(
#             simthresh = 0.80,
#             timeComparison = "rt",
#             rtdiff = .5,
#             RIdiff = 5,
#             minfeat = 2)
# metaSetting(TSQXLS.GC, "matchIrrelevants") <- list(
#             irrelevantClasses = c("Bleeding", "Plasticizers"),
#             timeComparison = "rt",
#             RIdiff = 2,    
#             rtdiff = .05,
#             simthresh = 0.70)
# metaSetting(TSQXLS.GC, "betweenSamples") <- list(
#             min.class.fraction = .5,
#             min.class.size = 5,
#             timeComparison = "rt",
#             rtdiff = .05,
#             RIdiff = 2,    
#             simthresh = .95)              
# ## End(Not run)