Biomedical Engineering Reference
In-Depth Information
..@ msnPrecursorIntensity : num(0)
..@ msnPrecursorCharge : num(0)
..@ msnCollisionEnergy : num(0)
..@ fi lepath : chr 'QC1_917_01.mzData'
..@ msnPrecursorIntensity : num(0)
..@ msnPrecursorCharge : num(0)
..@ msnCollisionEnergy : num(0)
..@ fi lepath : chr 'QC1_917_01.mzData'
We can then use various commands to determine the start and stop times,
mzrange and generate the TIC (total ion chromatogram) plot, shown in
Figure 4.2. It is also possible to output the raw data as a retention time
versus m/z versus intensity table as a CSV fi le.
RTstart=min(x1@scantime)
RTstart=min(x1@scantime)
RTstop=max(x1@scantime)
RTstop=max(x1@scantime)
RTstart
[1] 0.41058
RTstart
[1] 0.41058
RTstop
[1] 839.6642
RTstop
[1] 839.6642
x1@mzrange
[1] 85 900
x1@mzrange
[1] 85 900
#---------------------------------------------------------------
# To plot the TIC (Total Ion Chromatogram) use the getEIC method
#---------------------------------------------------------------
x2 <- getEIC(x1, mzrange=cbind(85,900),
rtrange = cbind(RTstart,RTstop),step = 0.1)
plot(x2)
#---------------------------------------------------------------
# To plot the TIC (Total Ion Chromatogram) use the getEIC method
#---------------------------------------------------------------
x2 <- getEIC(x1, mzrange=cbind(85,900),
rtrange = cbind(RTstart,RTstop),step = 0.1)
plot(x2)
#----------------------------------------------------------------------
# To extract a one Dalton wide Ion Chromatogram just change the mzrange
#----------------------------------------------------------------------
x2 <- getEIC(x1, mzrange=cbind(200.0,201.0), rtrange = cbind(1,800),
step = 0.1)
plot(x2)
#----------------------------------------------------------------------
# To extract a one Dalton wide Ion Chromatogram just change the mzrange
#----------------------------------------------------------------------
x2 <- getEIC(x1, mzrange=cbind(200.0,201.0), rtrange = cbind(1,800),
step = 0.1)
plot(x2)
#--------------------------------------
# To output the data as RT vs m/z table
#--------------------------------------
object <- rawMat(x1, mzrange = cbind(100.0,300.0),
rtrange = cbind(1,800),log=FALSE);
#--------------------------------------
# To output the data as RT vs m/z table
#--------------------------------------
object <- rawMat(x1, mzrange = cbind(100.0,300.0),
rtrange = cbind(1,800),log=FALSE);
write.csv(object, fi le='MStest.csv')
write.csv(object, fi le='MStest.csv')
“,'time','mz','intensity'
'1',1.55418,100.039428710938,10355.81640625
'2',1.55418,100.047500610352,1614.08435058594
'3',1.55418,100.050613403320,1042.66650390625
'4',1.55418,100.058731079102,487.58349609375
“,'time','mz','intensity'
'1',1.55418,100.039428710938,10355.81640625
'2',1.55418,100.047500610352,1614.08435058594
'3',1.55418,100.050613403320,1042.66650390625
'4',1.55418,100.058731079102,487.58349609375
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