Formula decomposition of higher masses #27
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Hi, I think compounds above 1000 Da (and with so many high mass fragments) are too much for the ILP. I would suggest that we compute high mass compounds with the heuristic. Yes, computing the exact solution is nice, but it is ridiculous that 99% of the running time of one analysis is spent on a few high mass compounds :/ |
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Hi Kai, I'm not sure about the mentioned heuristic, but I found a surprising outcome when testing in the NI mode (full spectra below). Here is the full input .ms file (same compound as in the first thread):
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BTW, If you need to retrain some model on higher mass compounds, I can generate 275 spectra of chemical standards with a mass range between 1001 and 1964 Da. I've taken Sebastian's comment from a few years ago and have increased the sensitivity of the peak extraction method - i.e. there are more low-mass putative fragments now. |
…mono-repo' into 'master' Resolve "Merge sirius-libs into sirius-frontend to create a mono repo." Closes #300, #132, #126, #123, #128, #125, #127, #124, #122, #121, #120, #109, #115, #106, #99, #112, #111, #61, #110, #103, #108, #107, #104, #221, #102, #98, #198, #92, #94, #93, #85, #84, #87, #76, #56, #73, #32, #70, #65, #43, #63, #33, #53, #58, #59, #57, #54, #52, #41, #47, #50, #49, #48, #39, #46, #37, #38, #27, #34, #22, #31, #28, #18, #23, #21, #19, #9, #240, #280, #254, #242, #246, #238, #156, #25, #155, #189, #172, #154, #11, #6, #16, and #4 See merge request bright-giant/sirius/sirius-frontend!106
Sirius team,
Apart from the blocking issues which seem (independently) be due to connection problems with the CSI server, I have a very slow convergence of the algorithm when running on .ms file of a larger compound of m/z=1388 corresponding with [M+NH4]+.
The running parameters where optimized for this situation - by reducing the PPM threshold and reserving sufficient resources - nevertheless the Sirius command line took roughly a day(!) to conclude, see:
The input spectra below, have you any idea? Maybe related to the Java run time parameters? Or to the large number of putative fragments (originating from DIA method)??
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