Open tobigithub opened 2 years ago
+1 on this issue and I'm pretty sure I have seen some QCxMS output some time which was in CSV form with these tables included. Did you follow up on this @tobigithub ?
@hechth I think we have a modified version or a parser for the output with formulas and also added a number of elements, @Shunyang2018 can you make the modified plotms repository public and post the link here? Basically we just parsed the res file added a few other elements and added the formulas to each line. This is similar to NIST23 MS/MS database output and extremely helpful because it confirms the formula for each calculated product ion, instead of having a mass error included.
Sure, I'm happy to help! Here is the public link: https://github.com/Shunyang2018/plot_msms_accurate I used a dictionary to save and update the formulas and intensities while parsing the .res file. Please let me know if you need more details!
Shunyang
On Fri, Oct 20, 2023 at 3:24 PM Tobias Kind @.***> wrote:
@hechth https://github.com/hechth I think we have a modified version or a parser for the output with formulas and also added a number of elements, @Shunyang2018 https://github.com/Shunyang2018 can you make the modified plotms repository public and post the link here? Basically we just parsed the res file added a few other elements and added the formulas to each line. This is similar to NIST23 MS/MS database output and extremely helpful because it confirms the formula for each calculated product ion, instead of having a mass error included.
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Maybe we can try to feed these improvements back upstream and make a pull request to the repo here?
Hi, this is for plotms 5.1. Also placeholder for potential merges from our development side.
For mass spectrometry experts it is extremely important to know the molecular formulas of the observed fragments. Because QCxMS produces such information it should be exported as table or independent file, but better should put into the JDX file.
Input res file is attached qceims.res.txt: Here is an example output for JDX with accurate masses and formulas.