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?
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
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.
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.
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?