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Messages
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Messages - jjjvanderhooft
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Vendor specific software / Re: Installation of Xcalibur on Windows 10 laptop
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Vendor specific software / Re: Installation of Xcalibur on Windows 10 laptop
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Vendor specific software / Installation of Xcalibur on Windows 10 laptop
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
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METLIN / Re: In Silico predicted MS spectra - A good idea?
The software used to generate the in-silico spectra is CFM-ID - you can find more info here: http://cfmid.wishartlab.com/
Thanks for notifying the community and METLIN on this :-)
Cheers Justin
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Vendor specific software / Re: Excalibur: Exporting exact mass list.
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
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XCMS Online / Re: Peak deconvolution and identification
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XCMS Online / Re: Peak deconvolution and identification
Hope this helps! Sorry there is no short and easy answer to this question :-)
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Early-career Members Network (EMN) / EMN webinar by Dr Emma Schymanski on small molecule databases and MS/MS searches
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Early-career Members Network (EMN) / EMN webinars
With thanks to Peter Meinkle for his excellent presentation!
Kind regards,
On behalf of the EMN and the MetSoc,
Justin
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Other / Re: Editing Wikipedia Metabolomics Page
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XCMS / Re: Peak filling - an example of strange results
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Compound identification / Re: A list of common neutral losses
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Compound identification / Re: A list of common neutral losses
That could grow to a very useful respository! Thanks for creating those - hope we will be able to add more in the nearby future....
Are those tables available as csv as well?
Cheers Justin
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Other / Re: Orbitrap AIF experiment - conversion of data to open format
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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