dear all!

I was trying various things with metabolomics data in xcms. In particular, I wanted to look at the total ion count (TIC), which, following http://www.ncbi.nlm.nih.gov/pubmed/25078324 is the "sum of all signals across all m/z" for a given retention time RT. A TIC can be generated using the plotTIC function in xcms, but, in order to get a feeling of the data, I wanted to generate the plot on the data myself. So I extracted the raw data matrix, summed up the intensity values per time point but to my surprise the plots look different, with the plotTIC resulting in higher intensities.

The code to generate the plots was:

> library(xcms)
> cdfpath <- system.file("cdf", package="faahKO")
> cdffiles <- list.files(cdfpath, recursive=TRUE, full.names=TRUE)
> xraw <- xcmsRaw(cdffiles[1], profmethod="bin", profstep=0.1)
> ## get the raw matrix and sum up the intensities per time point
> rawmat <- rawMat(xraw)
> aggr <- aggregate(rawmat, by=list(rawmat[, 1]), FUN=sum)
> ## plot the TIC
> plotTIC(xraw)
> points(aggr[, 1], aggr[, 4], col="red", type="l")

I can to some extend understand that plotTIC and plotChrom generate different plots, as plotTIC bases on the raw data and plotChrom on the profile data, but it puzzles me why there is a difference between the plotTIC and the sum of of intensities as I calculated them.

I think I am missing here something...

any help is very much appreciated

my session info:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin14.3.0/x86_64 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] lattice_0.20-31     xcms_1.45.0         ProtGenerics_1.0.0
[4] mzR_2.2.0           Rcpp_0.11.5         ascii_2.1          
[7] RColorBrewer_1.1-2  Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] compiler_3.2.0   tools_3.2.0      codetools_0.2-11

I can only give you my best guess as I'm not near a computer to test it out.

I'm quite sure this is true for mzXML/mzML files but uncertain with regards to cdf. Here goes: The file you're working with has a hard coded tic value for each scan that gets read in when you create an xcmsRaw object. This value comes from the instrument and is probably based on profile data. When you calculate it yourself you're working directly with the processed data and the results vary because of this.

Best Thomas