Re: [IDEOM forum]: Digest for ideom@googlegroups.com - 1 Message in 1 Topic

[Achuthanunni Chokkathukalam]

Hi Josh,

Sorry to hear that you are having trouble with mzMatch-ISO. I have now tried to run a single peakml file using your peptide.csv file and what is missing is the "id". I noticed that when you omit values in this column R mess up something somewhere! Furthermore, you are not required to have quotes around the values.

With data preparation part - you need to take it up to at least one combining step. This is because the software need sample group information for plotting and such. This is what I did, but you can also try giving an arbitrary group name as parameter (not tested).  Try with former first. Keep us posted if you have any other problems coming up.

Best Regards,

Unni

On 19 Mar 2013, at 10:39, id...@googlegroups.com wrote:

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• Targetted Isotope Quantification using mzMatch and xcms pipeline [1 Update]

 Targetted Isotope Quantification using mzMatch and xcms pipeline

Josh Goldford <gold...@umn.edu> Mar 18 03:27PM -0700  

Hello!
 
I am attempting to use R packages xcms and mzMatch on a Mac to identify 13C
labeled isotopes of HPLC separated peptides from an LTQ-Orbitrap Velos.
 
I am very new to R, but I have successfully worked through the example
provided on the following
webpage: http://mzmatch.sourceforge.net/isotopes-targetted.php.
 
My problem differs from the provided tutorial in that I do not have
biological replicates. That is, I simply have one .RAW file of MS1 spectra
collected in profile mode. I was given a list of peptides to search for in
the spectra, which came from an unlabeled MS/MS orbitrap experiment.
 
Currently, I am converting the .RAW file into an mzXML in centroid mode
using msconvert. I am using the following parameters for peak picking:
method="centWave",ppm=5,peakwidth=c(9,50),snthresh=1.
 
From my understanding of all the functions presented in the tutorial, I
have no further processing steps left given I only have one .RAW file (I
was hoping someone could verify this!)
 
After this, the .peakml file is generated
using PeakML.xcms.write.SingleMeasurement. I then attempt to
run PeakML.Isotope.TargettedIsotopes and get the following error:
 
Error in .jcall(java_project, returnSig = "D", method = "formulaToMass", :
java.lang.RuntimeException: Unknown element: A
 
I have attached the .csv file containing the peptides I am searching for.
I have checked to see if the .csv file was the issue, but when I use the
example .csv file "metlist_example.csv," I receive the same error. This
makes me think that there is a problem with the generation of the peakml
file.
 
Again, I am fairly new to R and Java, so I don't possess proper debugging
skills yet. Any help would be greatly appreciated!
 
Sincerely,
Josh

 

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