## import dataset install.packages(c("MALDIquant", "MALDIquantForeign")) library("MALDIquant") library("MALDIquantForeign") supportedFileFormats() s<-importBrukerFlex("C:/Users/Asus PC/Desktop/LCMS/Lab 1/group1/group1/Digest/Lowlaser") s intensity<- signature(object = "s", value = "numeric") intensity(s) #Quality Control any(sapply(s, isEmpty)) table(sapply(s, length)) length(s) all(sapply(s, isRegular)) plot(s[[1]]) plot(s[[2]]) plot(s[[3]]) plot(s[[4]]) plot(s[[5]]) plot(s[[6]]) plot(s[[7]]) #Variance Stabilization s <- transformIntensity(s,method="sqrt") #Smoothing s <- smoothIntensity(s, method="MovingAverage", halfWindowSize=10) plot(s[[1]]) plot(s[[2]]) plot(s[[3]]) plot(s[[4]]) plot(s[[5]]) plot(s[[6]]) plot(s[[7]]) #Baseline correction BC <- estimateBaseline(s[[3]], method="TopHat") plot(s[[3]]) lines(BC, col="red", lwd=2) plot(s[[1]]) plot(s[[2]]) plot(s[[3]]) plot(s[[4]]) plot(s[[5]]) plot(s[[6]]) plot(s[[7]]) #... and now we remove the baseline s <- removeBaseline(s, method="TopHat") plot(s[[1]]) plot(s[[2]]) plot(s[[3]]) plot(s[[4]]) plot(s[[5]]) plot(s[[6]]) plot(s[[7]]) #Intensity Calibration/normalization s <- calibrateIntensity(s, method="TIC") #Alignment s <- alignSpectra(s,halfWindowSize=20,SNR=2, tolerance=0.002, warpingMethod="lowess") s <- averageMassSpectra(s, labels=s, method="mean") #Peak Detection noise <- estimateNoise(s[[3]], method="MAD") plot(s[[3]], xlim=c(500, 3000), ylim=c(0, 0.02), main="Digest spectra after calibration", ylab="Intensity") lines(noise, col="red") lines(noise[,1], noise[, 2]*2, col="blue") peaks<-detectPeaks(s,method="MAD", halfWindowSize=20,SNR=2) plot(s[[3]],xlim=c(500,3000),ylim=c(0,0.01)) points(peaks[[3]],col="red",pch=4) #Peak Binning peaks<-binPeaks(peaks,tolerance=0.008) #Peak filtering peaks<-filterPeaks(peaks,minFrequency=0.25) featureMatrix <- intensityMatrix(peaks,s) head(featureMatrix) write.csv(peaks, "C:/Users/Asus PC/Desktop/LCMS/Lab 1/group1/group1/Digest/Lowlaser") #Just to see the Intact I<-importBrukerFlex("C:/Users/Asus PC/Desktop/LCMS/Lab 1/group1/group1/Intact") I plot(I[[1]]) plot(I[[2]], main="Intact mass spectra after calibration", ylab="Intensity") plot(I[[3]]) plot(I[[4]]) noise <- estimateNoise(I[[2]], method="MAD") plot(I[[2]], xlim=c(3000, 20000), ylim=c(0, 0.02)) lines(noise, col="red") lines(noise[,1], noise[, 2]*2, col="blue") peaks2<-detectPeaks(I,method="MAD", halfWindowSize=20,SNR=2) plot(I[[3]],xlim=c(500,3000),ylim=c(0,0.01)) points(peaks2[[2]],col="red",pch=4) plot(I[[2]],xlim=c(18060,18170),ylim=c(0,35000),)