Hi all, I am trying to use IPPD package to process peptide spectra from MALDI-TOF Brucker Ultraflextreme instrument. However, the model function seems to be poorly fit the real spectrum. Basically, I passed through the IPPD tutorial when analyzing data. The R code is presented below. library(IPPD) pl <- read.table("25-up-01_0_E14_1.txt", header=TRUE) x<-pl[,1] y<-pl[,2] y<-y[x>=500&x<=2500] x<-x[x>=500&x<=2500] gauss<-fitModelParameters( x,y, model="Gaussian", fitting=c("model"), formula.sigma=formula(~mz), control=list(window=6, threshold=200) ) emg<-fitModelParameters( x,y, model="EMG", fitting="model", formula.alpha=formula(~mz), formula.sigma=formula(~mz), formula.mu=(~1), control=list(window=6, threshold=200) ) mse.emg<-data.frame( mse=emg at peakfitresults[,2]/emg at peakfitresults[,1], peakshape=rep('EMG', nrow(emg at peakfitresults)) ) mse.gauss<-data.frame( mse=gauss at peakfitresults[,2]/gauss at peakfitresults[,1], peakshape=rep('Gaussian', nrow(gauss at peakfitresults)) ) mses<-rbind(mse.gauss,mse.emg) with(mses, boxplot(mse ~ peakshape, ylab='MSE')) dev.copy(png, 'MSE.png') dev.off() visualize(gauss) dev.copy(png, 'gauss_bestfit.png') dev.off() visualize(gauss, type='model', modelfit=TRUE) dev.copy(png, 'gauss_regression.png') dev.off() visualize(emg) dev.copy(png, 'emg_bestfit.png') dev.off() visualize(emg, type='model', modelfit=TRUE, parameters=c('alpha','sigma')) dev.copy(png, 'emg_regression.png') dev.off() emglist<-getPeaklist(x, y, model='EMG', model.parameters=emg, loss='L2', trace=FALSE, control.localnoise=list(factor.place=2), control.basis=list(charges=c(1,2)), control.postprocessing=list(ppm=200)) threshold(emglist, threshold=3, refit=TRUE, trace=FALSE) visualize(emglist, x,y,lower=1089, upper=1096) dev.copy(png, 'EMG_processed.png') dev.off() Model fitting statistics are in attachment. Can anybody suggest the points to work with for refining the model? -- Best regards, Yuri. -------------- next part -------------- A non-text attachment was scrubbed... Name: EMG_processed.png Type: image/png Size: 24451 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: MSE.png Type: image/png Size: 4678 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment-0001.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: gauss_regression.png Type: image/png Size: 7990 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment-0002.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: gauss_bestfit.png Type: image/png Size: 7140 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment-0003.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: emg_regression.png Type: image/png Size: 9775 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment-0004.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: emg_bestfit.png Type: image/png Size: 8262 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140120="" 487cd244="" attachment-0005.png="">