would it be possible to add some kind of location breadcrumb link to the forums? I mean something that indicates what forum I am in and allowing me to jump back. Say I am on http://www.metabolomics-forum.com/index.php?topic=1029.0 There should be a link on the top of the site that goes "Committees -> Publication committee" allowing me to directly go to those subforums. The links in "Jump to" at the bottom of the page are very hidden and inaccessible.
a question: Say I have raw high-resolution .mzML files in profile mode. I don't want to convert them to centroid mode because I want to retain the additional profile information present (e.g. for fine isotope analysis later on). Now I can open this file in R using mzR, and I have written a function which computes a centroid-mode spectrum for every scan.
How can I provide the centroided data (generated directly in R) to XCMS in an xcmsRaw-like object, so I can run centWave on it?
(One reason why I want to do this is that the error obtained by taking the local intensity maxima for the "centroid" m/z value can become quite large. The obtained m/z is much more accurate if I use e.g. an algorithm like the "Exact Mass" algorithm from MZmine, which takes the FWHM m/z value.)
We wanted to try the massifquant peak detection on some of our samples; apparently the findPeaks.massifquant function is not found in the DLL (the R part of the function seems to exist, it seems to fail when calling the DLL...)
fn <- "my_long_filename" # just to try: xs <- xcmsSet(fn, method="centWave") # works great. However: xs <- xcmsSet(fn, method="massifquant", ppm=5) 100309_pos_micropoll_19: Fehler in .Call("massifquant", object@env$mz, object@env$intensity, object@scanindex, : C Symbolname "massifquant" nicht in der DLL für Paket "xcms"
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.
> 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.
