Ok I found the problem. The line in the raw data I used to detect if an MS1 function was there have been changed with the new masslynx apparently. I really wonder how it could have worked with your other data.
So now my problem is that I don't see a really good way to detect MS1 anymore (as oppose to MS2). So I set it to assume that if there is no MSn then there is MS1.
I could probably find a better solution but I don't have time ATM to wrap my head around the very convoluted data waters writes.
The script below should work for you. Otherwise get back to me. Please check the output against what masslynx show just to verify that it is doing what it is suppose to.
Jan.
##############################################
## Settings (dirs have to use "/", not "")
##############################################
indir = 'C:/Users/jans/Desktop/ICHTYOSE_2013_06_07_2590'
outdir = 'C:/Users/jans/Desktop/ICHTYOSE_2013_06_07_2590/converted'
##############################################
##############################################
## Libraries
##############################################
library(xcms)
library(MetShot)
library(stringr)
##############################################
##############################################
## Functions
##############################################
no_scan_empty_warn <- function(w) if( any( grepl( "MS1 scans empty. Skipping profile matrix calculation.", w) ) )
invokeRestart( "muffleWarning" )
no_split_error_warn<- function(w) if( any( grepl( "MSn information will be dropped", w) ) )
invokeRestart( "muffleWarning" )
remakeTIC<-function(object){
object@tic<-numeric(length(object@scanindex))
for(i in 1:length(object@scanindex)){
object@tic[i]<-sum(getScan(object, i)[,"intensity"])
}
return(object)
}
LockMassFun_rem<-function(object,idx){
#idx<-AutoLockMass(object)
#idx=FindLockMass(object)
#select=c(0,1)
if(missing(idx)){stop('Parameters are missing')}
select=c(1,1)
# if (any(diff(idx)==1)){
# select=c(0,1)
# }else{
# select=c(1,1)
# }
idx.TF<-as.logical(rep(select, length(idx)/2))
idx.TF<-which(idx.TF != 0)
inx<-rep(TRUE, length(object@scanindex))
inx[idx[idx.TF]]<-FALSE
# separate scans into list
scans=list()
for (i in 1:length(object@scanindex)){
scans[[i]]=getScan(object,i)
}
# Just removed unwanted scans...
scans=scans[inx]
# Create new scanindex
scanindex_new=numeric()
for (i in 1:length(scans)){
if (i==1){
scanindex_new[i]=0
}else{
scanindex_new[i] = scanindex_new[i-1] + nrow(scans[[(i-1)]])
}
}
# Put data into new object
ob<-new("xcmsRaw")
ob@env = new.env(parent=.GlobalEnv)
scans=do.call(rbind,scans)
ob@env$mz<-scans[,'mz']
ob@env$intensity<-scans[,'intensity']
ob@scantime <-object@scantime[inx]
ob@scanindex <-as.integer(scanindex_new)
ob@polarity <- object@polarity[inx]
ob@acquisitionNum <- 1:length(ob@scanindex)
ob@profmethod <- object@profmethod
ob@mzrange <- object@mzrange
ob@filepath <- object@filepath
profStep(ob) = profStep(object)
ob=remakeTIC(ob)
return(ob)
}
LockMassFun_rep<-function(object,idx){
#idx<-AutoLockMass(object)
#idx=FindLockMass(object)
#select=c(0,1)
if(missing(idx)){stop('Parameters are missing')}
select=c(1,1)
# if (any(diff(idx)==1)){
# select=c(0,1)
# }else{
# select=c(1,1)
# }
idx=idx[idx>1] # We don't allow to replace scan 1 since there is nothing before to replace with
idx.TF<-as.logical(rep(select, length(idx)/2))
idx.TF<-which(idx.TF != 0)
inx<-rep(TRUE, length(object@scanindex))
inx[idx[idx.TF]]<-FALSE
# separate scans into list
scans=list()
for (i in 1:length(object@scanindex)){
scans[[i]]=getScan(object,i)
}
# Here we do the fillin instead
for (i in idx[idx.TF]){
scans[[i]]=scans[[i-1]]
}
# Create new scanindex
scanindex_new=numeric()
for (i in 1:length(scans)){
if (i==1){
scanindex_new[i]=0
}else{
scanindex_new[i] = scanindex_new[i-1] + nrow(scans[[(i-1)]])
}
}
# Put data into new object
ob<-new("xcmsRaw")
ob@env = new.env(parent=.GlobalEnv)
scans=do.call(rbind,scans)
ob@env$mz<-scans[,'mz']
ob@env$intensity<-scans[,'intensity']
ob@scantime <-object@scantime
ob@scanindex <-as.integer(scanindex_new)
ob@polarity <- object@polarity
ob@acquisitionNum <- object@acquisitionNum
ob@profmethod <- object@profmethod
ob@mzrange <- object@mzrange
ob@filepath <- object@filepath
profStep(ob) <- profStep(object)
ob=remakeTIC(ob)
return(ob)
}
MSnSplit<-function(object,f){
ob = withCallingHandlers( split(msn2xcms(object), f )$'TRUE' , warning = no_split_error_warn )
ob@env$msnIntensity = ob@env$intensity
ob@env$msnMz = ob@env$mz
ob@tic = numeric()
ob@msnScanindex = ob@scanindex
ob@scanindex = integer()
ob@scantime = numeric()
ob@acquisitionNum = integer()
ob@mzrange = numeric()
ob@msnAcquisitionNum = ob@msnAcquisitionNum[f]
ob@msnPrecursorScan = ob@msnPrecursorScan[f]
ob@msnLevel = ob@msnLevel[f]
ob@msnRt = ob@msnRt[f]
ob@msnPrecursorMz = ob@msnPrecursorMz[f]
ob@msnPrecursorIntensity = ob@msnPrecursorIntensity[f]
ob@msnPrecursorCharge = ob@msnPrecursorCharge[f]
ob@msnCollisionEnergy = ob@msnCollisionEnergy[f]
return(ob)
}
MSnExtractLockmass<-function(object,MSparam=NULL){
if (missing(MSparam)){stop('MSparam has to be set.')}
lockmass=grep('Lock Mass',MSparam)
if (!(length(lockmass)==0)){
lockmass=MSparam[lockmass[length(lockmass)-1]]
lockmass = strsplit(lockmass,"t")
lockmass = as.numeric(lockmass[[1]][length(lockmass[[1]])])
}else{
lockmass=grep('EDC Mass',MSparam)
lockmass=MSparam[lockmass]
lockmass = strsplit(lockmass,"t")
lockmass = as.numeric(lockmass[[1]][length(lockmass[[1]])])
}
lockhist_freq = as.matrix(table(object@msnPrecursorMz))
lockhist_masses = as.numeric(rownames(lockhist_freq))
lockhist_masses = lockhist_masses[ which.min(abs(lockhist_masses-lockmass)) ]
return(lockhist_masses)
}
##############################################
##############################################
## Get file list
##############################################
files = list.files(indir, pattern='.raw', full.names=T)
namelist=character()
filenames=character()
log_convert = list()
log_warnings=character()
log_convert_warning = list()
log_convert_warning[[1]]=' '
##############################################
for (i in 1:length(files)) {
##############################################
## Check if lockspray is present. TODO: Scream at waters
##############################################
input_method = scan(paste(files[i],'/_extern.inf',sep=""), character(0), sep = "n",quiet=T)
lockspray_present = any(grepl('Lock Spray Configuration',input_method))
if (!lockspray_present){
warning(paste('LockMass seems to be disabled for file ',basename(files[i]),'!', ' Saving data as is.',sep=""),immediate. = T)
}
##############################################
##############################################
## Get name of sample
##############################################
name = scan(paste(files[i],'/_HEADER.TXT',sep=""), character(0), sep = "n",quiet=T)
name_where = grepl('Sample Description',name)
namelist[i] = strsplit(name[name_where],': ')[[1]][2]
rm(name,name_where)
##############################################
##############################################
## Get polarity
##############################################
ionmode = scan(paste(files[i],'/_extern.inf',sep=""), character(0), sep = "n",quiet=T)
if (!(any(grepl('ES+',ionmode,fixed = T)) | any(grepl('ES-',ionmode,fixed = T)))){warning('Ionization mode cannot be detected!')
}else{
if(any(grepl('ES+',ionmode,fixed = T))){ionmode='positive'
}else{ionmode='negative'}
}
##############################################
##############################################
## Get the functions and figure if there is MS1, MSn and/or MSE
##############################################
func_start = grep('Function Parameters - Function',input_method,fixed=T)
func_end = c( grep('Function Parameters',input_method,fixed=T)-1 , length(input_method) )
func_end = func_end[ 2:length(func_end) ]
MSE=F
MSn=F
MS1=F
functions=list()
for (i2 in 1:(length(func_start))){
functions[[i2]]=input_method[ func_start[i2]:func_end[i2] ]
}
not_ref = unlist(lapply(functions, function(x) !grepl(' - REFERENCE',x[1])))
MSn = any(unlist(lapply(functions, function(x) grepl('TOF MSMS FUNCTION',x[1],fixed=T))))
# MS1 = any(unlist(lapply(functions, function(x) grepl('TOF MS FUNCTION',x[1],fixed=T))))
# MS1 = any(unlist(lapply(functions, function(x) grepl('Trap MS Collision Energy (eV)ttt4.0',x,fixed=T))))
if (!MSn){MS1=T}
if (!MSn){
for (i2 in which(not_ref)){
if (any(grepl('Collision Energy Ramp Start',functions[[i2]],fixed=T))){
MSE=T
}
}
}
##############################################
##############################################
## Convert the data
##############################################
tempfile = tempfile(pattern = basename(gsub('.raw','',files[i])), tmpdir = '/', fileext = ".mzXML")
# if there is mobility data we need to make a copy and remove it. Otherwise masswolf doesn't work
if (file.exists( paste( files[i],'/apex3D',sep=''))){
input_file= paste( gsub('.raw','',files[i],fixed=T),'_temp.raw',sep='')
dir.create(input_file)
to_copy=list.files(path = files[i], all.files = T,full.names = T, recursive = F,ignore.case = T, include.dirs = T,no.. = T)
to_copy=to_copy[ !(grepl('/_mob',to_copy,fixed=T) | grepl('/apex3D',to_copy,fixed=T) | grepl('.cdt',to_copy,fixed=T) | grepl('.ind',to_copy,fixed=T)) ]
temp=file.copy(to_copy, input_file,overwrite=F,recursive=T)
rm(temp)
}else{
input_file= files[i]
}
# Convert with mass wolf
if (MSE){
log_convert[[i]]=system(paste('masswolf --MSe --mzXML ',""",input_file,""",' ',""",outdir,tempfile,""",sep=""), intern=T)
}else{
log_convert[[i]]=system(paste('masswolf --mzXML ',""",input_file,""",' ',""",outdir,tempfile,""",sep=""), intern=T)
}
# Delete temporary file of created (for files that include mobility data)
if (file.exists( paste( files[i],'/apex3D',sep=''))){
unlink(input_file,recursive=T)
}
# Read the raw Waters data
raw_file_data = scan(paste(outdir,tempfile,sep=''), character(0), sep = "n",quiet=T)
scan_start = grep('<scan num=',raw_file_data,fixed=T)
scan_end = c( scan_start[2:length(scan_start)]-1 , length(raw_file_data) )
raw_file_data_scans=list()
for (i2 in 1:(length(scan_start))){
raw_file_data_scans[[i2]]=raw_file_data[ scan_start[i2]:scan_end[i2] ]
}
##############################################
##############################################
## Read retention times and scan numbers in original data
##############################################
# Get scan retention times
raw_file_data_ret = lapply(raw_file_data_scans, function(x) as.numeric(str_trim(str_replace(str_replace(x[ grep('retentionTime',x) ],'retentionTime="PT', ''),'S"',''),side='both')) )
raw_file_data_ret = unlist(raw_file_data_ret)
# Get which are lockmass (calibration) scans
is_lockmass_scan = lapply(raw_file_data_scans, function(x) any(grepl('scanType="calibration"',x,fixed=T)) )
is_lockmass_scan = unlist(is_lockmass_scan)
# Get which are MSE or MS2 scans
#is_MSE_or_MSn_scan = lapply(raw_file_data_scans, function(x) any(grepl('msLevel="2"',x,fixed=T)) )
#is_MSE_or_MSn_scan = unlist(is_MSE_scan)
##############################################
##############################################
## Read file
##############################################
xr_org = withCallingHandlers( xcmsRaw(paste(outdir,tempfile,sep=""),includeMSn=T), warning = no_scan_empty_warn )
##############################################
##############################################
## if it is an MSE file, write seperate MSE file
##############################################
if (MSE){
xr_MSE =new('xcmsRaw')
xr_MSE@env = xr_org@env
xr_MSE@msnScanindex = xr_org@msnScanindex
xr_MSE@msnAcquisitionNum = xr_org@msnAcquisitionNum
xr_MSE@msnPrecursorScan = xr_org@msnPrecursorScan
xr_MSE@msnLevel = xr_org@msnLevel
xr_MSE@msnRt = xr_org@msnRt
xr_MSE@msnPrecursorMz = xr_org@msnPrecursorMz
xr_MSE@msnPrecursorIntensity = xr_org@msnPrecursorIntensity
xr_MSE@msnPrecursorCharge = xr_org@msnPrecursorCharge
xr_MSE@msnCollisionEnergy = xr_org@msnCollisionEnergy
xr_MSE@filepath = xr_org@filepath
filename=basename(gsub('.raw','_MSE.mzData',files[i]))
write.mzdata(xr_MSE,paste(outdir,'/',filename,sep=""))
}
##############################################
##############################################
## Write MS1 data
##############################################
if (MS1){
if (lockspray_present){
idx=match(raw_file_data_ret[is_lockmass_scan],xr_org@scantime)
idx = idx[!is.na(idx)]
xr_fixed=LockMassFun_rep(xr_org,idx)
xr_fixed@polarity=factor(rep(ionmode,1,length(xr_fixed@polarity)),levels=c('negative','positive','unknown'))
}else{
xr_fixed=xr_org
xr_fixed@polarity=factor(rep(ionmode,1,length(xr_fixed@polarity)),levels=c('negative','positive','unknown'))
}
# Write fixed file
filenames[i]=basename(gsub('.raw','.mzData',files[i]))
write.mzdata(xr_fixed,paste(outdir,'/',filenames[i],sep=""))
temp1 = plotChrom(xr_org)
temp2 = plotChrom(xr_fixed)
}
##############################################
##############################################
## Write MSn data
##############################################
if (MSn){
if (lockspray_present){
LockMass = MSnExtractLockmass(xr_org,MSparam=input_method)
f = xr_org@msnPrecursorMz != LockMass
if(any(f)){
log_convert_warning[length(log_convert_warning)+1]=print(paste('Lockmass detected at ',formatC(LockMass,digits=7),'Da in range ',format(min(xr_org@msnRt[f])/60,digits=2),'min to ',format(max(xr_org@msnRt[f])/60,digits=2),'min for file: ',basename(files[i]),sep=""))
xr_fixed = MSnSplit(xr_org,f)
xr_fixed@polarity=factor(rep(ionmode,1,length(xr_fixed@polarity)),levels=c('negative','positive','unknown'))
}else{
log_convert_warning[length(log_convert_warning)+1]=print(paste('Lockmass was enabled but no lockmass scans could be found. Data written as is for file: ',basename(files[i]),sep=""))
xr_fixed=xr_org
}
}else{
xr_fixed=xr_org
xr_fixed@polarity=factor(rep(ionmode,1,length(xr_fixed@polarity)),levels=c('negative','positive','unknown'))
}
# Write fixed file
filenames[i]=basename(gsub('.raw','.mzData',files[i]))
write.mzdata(xr_fixed,paste(outdir,'/',filenames[i],sep=""))
temp1=msn2xcms(xr_org)
temp1=remakeTIC(temp1)
temp1=plotTIC(temp1)
temp2=msn2xcms(xr_fixed)
temp2=remakeTIC(temp2)
temp2=plotTIC(temp2)
}
##############################################
##############################################
## Debugging plots
##############################################
## debugging, plotting
dir.create(paste(outdir,'/debug/',sep=""),showWarnings=F)
png(paste(outdir,'/debug/',basename(gsub('.raw','.png',files[i])),sep=""),width=2000,height=1500,res=300)
plot(temp1,type='l',col='red',xlim=c(-10,max(temp1[,1])))
lines(temp2,col='green')
dev.off()
rm(temp1,temp2)
# delete temp file
unlink(paste(outdir,tempfile,sep=""))
rm(xr_org,xr_fixed)
gc()
log_warnings[i]=warnings()
}
##############################################
write.csv(cbind(filenames,namelist),paste(outdir,'/','filelist.csv',sep=""))
fileConn<-file(paste(outdir,'/','log_convert.log',sep=""))
writeLines(unlist(log_convert), fileConn)
close(fileConn)
fileConn<-file(paste(outdir,'/','log_warnings.log',sep=""))
writeLines(unlist(as.character(log_warnings)), fileConn)
close(fileConn)
fileConn<-file(paste(outdir,'/','log_convert_warning.log',sep=""))
writeLines(unlist(log_convert_warning), fileConn)
close(fileConn)
