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Messages - jjjvanderhooft

1
XCMS / Re: mz > 1000
Check the settings of your acquisition method - 1000 is often used as higher end cut-off for the mass window. Also, the tuning influences the number of peaks you will detect above m/z 1000....
4
Vendor specific software / Installation of Xcalibur on Windows 10 laptop
Hi,

Does anybody has experience trying to install Xcalibur software on a Windows 10 machine?
I run into DLL issues - the program wouldn't open or get deleted from the laptop without 'forceful' handling.
Are there any patches around to fix this?
It was the newest version 4.0.27 that I am trying to run....

Thanks for advice,

Justin


6
Vendor specific software / Re: Excalibur: Exporting exact mass list.
Hi Jeremy,

Try to copy it through the peak list rather than directly from the spectrum. After displaying the peak list, you can copy that (by right-mouse click) in exact mass or nominal mass to the clipboard.
The mass options you mention do not influence the numbers you copy - the numbers you copy are the measured values - those mass options are to display any ions within the given ppm range for a mass range or base peak chromatogram.

Hope this helps.,

Justin
8
XCMS Online / Re: Peak deconvolution and identification
Hi @LiseD , that is a good question. If such a package would exist, than lots of metabolomics researchers would be out of work. There is plenty of literature that can help you on the way on how to identify/annotate the different metabolites in your sample. If you run standards with your experiments, it would be a good start to see if they co-elute with any of the LC-MS peaks in your sample. Then, you could use literature data to find masses (and perhaps an indication of the retention times) of expected metabolites and see if you can find any potential matches. Be careful, however, as a match based on mass (or most likely elemental formula), is no definite identification. For an overview of (quite) recent metabolomics tools, see: http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract For more information on metabolite ID using mass spectrometry data, see papers like http://link.springer.com/article/10.1007/s11306-013-0519-8 (and refs therein) and http://pubs.acs.org/doi/abs/10.1021/ac503325c
Hope this helps! Sorry there is no short and easy answer to this question :-)
15
Other / Re: Orbitrap AIF experiment - conversion of data to open format
Hi Marynka,

It seems awkward that the mzXML files do not include the fragmentation files. When you say 'msconverter', do you mean 'MSconvert' from ProteoWizard? (see image attached of the GUI) If you use that, double-check that you do not filter out any MS2 scans, as it is possible to do so. With the settings as displayed, it should not do so and include all scan events of level '1' (full scan) and higher....
After reading in all the files, the scan header information contains the necessary information (like retention time etc.) to 'connect' or 'place' the scan events. 

I think there is currently a lack of software that deals with AIF data. You might have heard of MS-DIAL (http://www.nature.com/nmeth/journal/v12/n6/full/nmeth.3393.html) which combines the full scan data with the fragmentation data present in the AIF scan events to reconstruct MS1-MS2 pairs (by deconvolution) as if data-dependent analysis was done.

Hope this helps and otherwise I hope people with AIF data processing experience will share their solutions!

Good luck,

Cheers Justin




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