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Messages - Arjen_vanDoorn

1
XCMS Online / Re: Wiff file issues
For the sake of completion, here is the code I use to convert a directory of MS-convert MZml files to .cdf files, in case someone else runs into the same problem and has quite a few samples. Courtesy of Steffen Neumann, he gave me the script a few weeks ago.

Code: [Select]
library(xcms)
    files <- list.files(pattern="*.mzML")
     for (file in files) {
         mzdata <- paste(file, ".mzData", sep="")
         if (! file.exists(mzdata)) {
             xr <- xcmsRaw(file)
 			scans <- length(xr@scanindex)
 			tags <- c("MS1", "MS1B", "MS2A", "MS2B")
 			f <- rep(tags, scans/length(tags)+1)[1:scans]
 			xrs <- split(xr, f=f)
 			xr1 <- xrs[["MS1"]]
 			write.cdf(xr1, sprintf("MS1_%s.cdf", file))  
     }
     }
2
XCMS Online / Re: Wiff file issues
Hi all, thanks so much for your help!

One (naive) question on the splitten.R, is the peakpicking at this step necessary, or can I write directly to cdf? I'd rather do the peakpicking of the whole dataset (24 samples) at once, not file-by-file, and since the computer I have is "not optimized" for number-crunching everything goes rather slow, and the peakpicking take quite some time.

Thanks again, this really helps - the software from ab-sciex is pretty with colours and lots of buttons, but it can't really do basic stuff...
3
XCMS Online / Re: Wiff file issues
Hi Ralf,

Thanks so much for looking at the data, really helpful! I'll contact Matt to see if he's known with the issue, and will keep asking AB SCIEX for a proper solution. Could you also see a 5th level in the files, there should be a trace of DAD array in there as well. I guess that proteowizard is part of the pipeline for xcms-online, and thus it doesn't work either when I directly upload the .wiff files.

Anyway, I'll see what the guys at proteowizard can do, otherwise I'll have to extract the relevant data myself out of the files.
4
XCMS Online / Re: Wiff file issues
Hi Ralf,

Thanks for your answer, I used the parameters for the machine I used (UPLC/TripleTof pos), hope this is ok.

I can send you a file, I've send you a PM via the forums to give you my email address.
5
XCMS Online / Wiff file issues
Hello,

I've got some strange problems with .Wiff files from an AB SCIEX triple-quad machine that I'm trying to analyze. The files I have contain multiple MS levels (we need to exclude a contaminant ion, so we analyze m/z 50-180 and 190-1200, both at 2 different energies), as well as the trace from the DAD detector, making 5 traces. I can analyze this data fine in (proprietary) software such as MarkerView, but I'd prefer to use xcms since I need to features that are not available in MarkerView.

Now, I've tried to upload the .Wiff and the .wiff.scan files, and submitted a job, but I get this error:

Quote
There were no features detected in at least one of your samples. Please check feature detection settings and make sure the selected method is applicable for your data.

However, if I look in PeakView, the AB SCIEX software that can read .wiff files, I can clearly see features, an image from some random extracted ion is here:


It may not look the best, but it should be able to find some features in such a file...

I have the idea that it is a problem with the multiple MS levels that are stored in a single file, also because I could no-where specify which level it should use for the analysis. Unfortunately, the translat.exe that should be able to convert the .wiff files to .NETcdf files for each channel is not working, the AB SCIEX MS data converter can only create .mzml files containing all channels, or .MGF files that can only read MS/MS data. If try to convert that data with Proteowizard to MzXML files, I select the right file format, choose 32 bit, and enable compression, select 'peak picking' and add MS-level 1-1- it subsequently creates files that are 1.4 GB large, which is frankly absurd for a 40-min MS1 run in centroid mode. XCMS under R can't do anything with that file either, it gives a memory error.

Does anyone here have any experience with .wiff files containing multiple MS levels? Any help will be greatly appreciated!