Metabolomics Society Forum

xs <- xcmsSet(whatever)
# see first peak
print(xs@peaks[1,])
# subtract a constant shift (30 sec) from all rt values:
shift <- 30
xs@peaks[,c("rt", "rtmin", "rtmax")] <- xs@peaks[,c("rt", "rtmin", "rtmax")] - shift
# print the modified peak
print(xs@peaks[1,])

# then there's also the xs@rt which one could shift, 
# but I don't know whether that's needed for the remaining workflow -
# I believe all further calculations start from xs@peaks.
xs@rt <- xs@rt - shift

package(XML)

openXML.mzML <- function(filename)
{
	mzml <- xmlTreeParse(filename, asText=F, useInternalNodes=T,
			fullNamespaceInfo=T,useDotNames=T)
	return(mzml)
}

getConfigs.mzML <- function(mzml)
{
	instrumentConfigs <- getNodeSet(mzml,
			"/m:indexedmzML/m:mzML/m:instrumentConfigurationList/m:instrumentConfiguration",
			c(m="http://psi.hupo.org/ms/mzml"))
	
	configs <- t(sapply(instrumentConfigs, function(ic){
						id <- xmlAttrs(ic)[["id"]]
						analyzer <- getNodeSet(ic, "m:componentList/m:analyzer/m:cvParam",
								c(m="http://psi.hupo.org/ms/mzml"))
						analyzerName <- xmlAttrs(analyzer[[1]])[["name"]]
						analyzerMSO <- xmlAttrs(analyzer[[1]])[["accession"]]
						return(c(id, analyzerName, analyzerMSO))
					}))
	
	rownames(configs) <- configs[,1]
	colnames(configs) <- c("ID", "name", "ontology")
	return(configs)
}

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=German_Switzerland.1252  LC_CTYPE=German_Switzerland.1252   
[3] LC_MONETARY=German_Switzerland.1252 LC_NUMERIC=C                       
[5] LC_TIME=German_Switzerland.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mzR_1.3.7    Rcpp_0.9.11  devtools_0.7

loaded via a namespace (and not attached):
 [1] Biobase_2.17.6     BiocGenerics_0.3.0 codetools_0.2-8    digest_0.5.2      
 [5] httr_0.1.1         memoise_0.1        plyr_1.7.1         RCurl_1.91-1.1    
 [9] stringr_0.6        tools_2.15.1      
d> 

# from xcmsRaw:
xraw <- xcmsRaw("myfile.mzML")
# by FWHM method: 
xraw.sticked <- deprofile.xcmsRaw(xraw, copy=T, method="deprofile.fwhm")
# local maximum: faster, but less accurate especially for "low" resolution
xraw.sticked <- deprofile.xcmsRaw(xraw, copy=T, method="deprofile.localMax")
scan.xraw.profile <- getScan(xraw, 50)
scan.xraw <- getScan(xraw.sticked, 50)
# alternatively directly from scan:
scan.xraw.direct <- deprofile.scan(scan.xraw.profile)

# this can be peakpicked:
xpeaks <- findPeaks(xraw.sticked, method="centWave", ppm=5, snthresh=10, noise=3000, prefilter=c(3,5000))

# the same scan from mzR:
mzrFile <- openMSfile("myfile.mzML")
acqNo <- xraw@acquisitionNum[[50]]
scan.mzML.profile <- mzR::peaks(mzrFile, acqNo)
scan.mzML <- deprofile.scan(scan.mzML.profile) 
close(mzrFile)