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Topics - drchrispook

1
Pathway analysis / CHEBI hierarchy
Hi, I'm trying to apply this very cool pathway analysis to my lipidomics data.
https://pubmed.ncbi.nlm.nih.gov/36376837/

My problem is that CHEBI IDs for lipids are difficult to find in databases as the ones used in the Reactome pathways are often high-level  generalised ones. Eg. https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17815 is a generic 1,2-diglyceride. When I search for matches in Reactome for my diglyceride annotations, they don't match as they are for specific DG species. Is there a hierarchical system by which I can find matches for my specific annotations, as well as any entries in CHEBI for higher ontological classes?

To complicate matters further, there is a separate entry for a diglcyeride with unspecified positions https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A18035, and a third for diradylglycerides with unspecified r-groups that may be acyl, https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A76578.
2
MS-DIAL / RT correction
Has anyone used RT correction successfully? I can see that it works to align the shifted peaks from my two batches of analysis (see RT_correction screenshot) but the peaks are distorted. See other pics for examples. Won't this affect quantification?
I'm running v4.9.221218
Thanks,
 Chris
3
MS-DIAL / MS-DIAL v4.92 lipid ontologies are incorrect
In case anyone else is relying on these for filtering their data, lysophosphatidylcholines are being classified as HexCer_NDS and phosphatdylchlines as OxTG. These are obviously incorrect. I haven't tested this in any other versions.
4
MS-DIAL / msp export of DDA data for MS-FINDER doesn't contain MS1 spectrum
Hi, the export function for .msp in v4.80 doesn't write the MS1 spectrum to the file. See attached screenshot of example data. I think this is important for formula inference. The MS1 spectrum is present in the alignment export though so the information just isn't being written.
Regards,
Chris


EDIT 5 minutes later: This is my error. If you want the MS1 spectrum as well as MS2 then you can't export to .msp format because it only holds a single spectrum. Export in .mat format instead using the "Export" button instead of the "Save as MSP" button. See highlight in my second image.
5
MS-DIAL / MS-DIAL and MS-FINDER library limits
Hello,

I have converted the 2020 NIST HR-MSMS library to .msp format and tried using it in MS-DIAL and MS-FINDER. I had to amend some keys as the NIST ones didn't match that of the MS-DIAL libraries. Once I had done this small subsets of the entire NIST library worked. However the whole library (3Gb) doesn't provide any annotations in MS-DIAL or MS-FINDER. Is there a limit to the size of a .msp file these programs can use? Is there some way that I can test to see if MS-DIAL or MS-FINDER are loading the library correctly?

Thanks in advance.
Chris