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I’m processing GC data in with PCI ionization in Compound Discoverer 3.2 and would like to just get the deconvoluted spectra into excel so I can write code to align it with EI data but I don’t see a way to export all the deconvoluted features which includes mass:intensity pairs of the spectra. I am able to export the data I need for a single spectrum but not all of them at once and I’m not going to manually export hundreds of spectra one at a time.
Also, I’m able to do this in MSDial but I’d love to keep using compound discoverer. The mass intensity pairs I’m trying to get look like this:
351.26724:156988 352.27059:184363 353.27395:121612
and there is one for each feature. Thanks for any help.
I think I know of a long way to do this by building a mzVault library in CD of the features you want (I usually mark them with the colored “tags” on the far left hand side). Once you have all your features in the Compounds Table, right click and “build mzVault library”. Then go to the Lists and Libraries Manager, find your new mzVault library in the Spectral Libraries tab, and export it. Then open up mzVault and load your new database file and export from there into excel. That will give you (in a big table that needs reformatting to get to the desired format mentioned in the OP) precursor m/z and fragment m/z with “target” ratios, but in this case since it’s experimental data you used to make the library, it’s observed target ratios.
@gpblack – thanks! I will try that. We were told “m/z vault doesn’t handle GC data” which is silly to me. But this is worth a try. I’ll let you know how it goes
@gpblack – check the attached picture (sorry for poor quality). I don’t see any options to “Build mzVault Library”. Am I looking in the right place?
Shoot, it should be in that dropdown menu. Unless you can export as that NIST MSP option and open that in mzVault, I don’t think my workaround will work :/
I know Logan Roach with James McCord has been working on an R script to process spectra and send them off to Tony Williams. I’m pretty sure he was starting from spectra in Compound Discoverer, so he must have a method of exporting the desired MS2 spectra from Compound Discoverer directly.
High Jargon Answer: You can directly access the spectra from the SQLite database and parse the spectra binary streams to produce a text output in whatever format you need.
Low Jargon Answer: Your results file has the spectra stored in a compressed format and Thermo doesn’t have a way to export them. As boettger mentioned, I have a script that pulls out spectra from an mzVault file, but the same method should work to pull them out of a CD results file. I would just need a test file to work with and some spare time to modify the script. If you send me an email or share a test file I can try to scrape something together.
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