TIC of MS/MS spectra?

Topic: TIC of MS/MS spectra? (Read 4722 times) previous topic - next topic

TIC of MS/MS spectra?

November 04, 2011, 09:51:04 AM

Hi,

I'm basically trying to extract the TIC for each single MS/MS scan from my data file.

I tried using the xcmsRaw class, loading the MSMS data to the "main level" and looking at the TIC slot, but it appears to be empty (see code below; all other information seems to be correct.) Also, I don't understand what the warning message is telling me - is the function supposed to be used differently? Using mslevel=2 without includeMSn=TRUE returns NULL.

Code: [Select]

> xrmsms <- xcmsRaw(fileName, includeMSn=TRUE,mslevel=2)
Warnmeldung: In split.xcmsRaw(object, f = object@msnLevel == mslevel) :  MSn information will be dropped
> length(xrmsms@tic)
[1] 2562
> which(xrmsms@tic != 0)
integer(0)
> which(xrmsms@scantime != 0)
   [1]    1    2    3    4    5    6 etc etc until 2562

I would need this data to merge it with a dataframe generated from @msnScanindex and @msnPrecursorMz so that I could then filter out the intensity of the tandem spectra for one selected mass.

Any suggestions?

Re: TIC of MS/MS spectra?

Reply #1 – November 08, 2011, 12:41:12 AM

Hi meow,

The split(xcmsRaw, factor) function is intended to split the "normal" MS1 scans.
How should it know which MSn goes to which of the split'ed new xcmsRaws ?
(Actually, it could possibly do so if the parent scan is properly annotated).
But it is not intended to split those MSn scans into several xcmsRaw's .

Instead, I'd suggest to do some sapply(), getMsnScan() and sum().
I have just started to fix getMsnScan(), in xcms 1.31.1 and will keep you posted.

Yours,
Steffen

Re: TIC of MS/MS spectra?

Reply #2 – November 08, 2011, 03:41:04 AM

Hi Steffen,

I looked into the source code to understand the issue.

Actually, my actual "problem" is caused by msn2ms (xcmsRaw.R, line 1873):

Code: [Select]

    object@tic <- rep(0, length(object@msnAcquisitionNum)) ##

msn2ms just fills my TIC data with zeroes... apparently this is because the data is never read into xcmsRaw in the first place. Is there a special reason for this? The mzXML files themselves do contain the information.

---------------------------------------------
Concerning split.xcmsRaw: I now see why the function gives this warning in general. However, I did not call the split function myself; it is called by xcmsRaw(..., mslevel=2), xcmsRaw.R, line 85, where the xcmsRaw object is split into the TRUE and FALSE datasets (TRUE being all entries which have the correct @msnLevel).

The warning additionally confused me because MSn data is actually never dropped; it is just copied over verbatim without being split. (xcmsRaw.R, line 1809). Is this intended?

From an user perspective, it is not obvious why calling a method which is meant to transfer MSn data to MS1 slots (i.e. xcmsRaw(..., msLevel = n) results in a warning about MSn data being dropped (irrespective of whether or not the data is actually dropped)... Would it maybe make sense to suppress the warning in this case?

Best,
-Michael