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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Different results for the same metabolite #158

Open shitianhuo opened 3 weeks ago

shitianhuo commented 3 weeks ago

hello I am analyzing the same metabolite using sirius 5.8.7 and 6.0.0 respectively, but it gives two different results, while sirius 5.8.7 gives the correct result, why is that? image image thanks

shitianhuo commented 3 weeks ago

I found that when choosing the parameter De novo + bottom up, it gives incorrect results, so which parameter should I choose for a large number of analyses?

kaibioinfo commented 3 weeks ago

Hi, can you provide the spectrum for this compound?

In general, the bottom-up method (from Buddy, Xing et al. 2023) should work like a "extended database" search and is some kind of "sweet spot" between "just searching in a database" (and missing some annotations) and running fully de-novo (which takes MUCH more time).

If you want to use CSI:FingerID afterwards to get structure annotation, you might just use database search instead of bottom-up and de-novo.

De novo formula annotation is more important if you really want to annotate unknown unknowns which are not contained in any databases.

Nevertheless, I would like to find out why SIRIUS 5.8 annotation is better here. So if you can share the spectrum I will take a look.

shitianhuo commented 3 weeks ago

BEGIN IONS FEATURE_ID=467 PEPMASS=700.1352 SCANS=467 RTINSECONDS=110.479 CHARGE=1- MSLEVEL=2 MERGED_STATS=1 / 1 (0 removed due to low quality, 0 removed due to low cosine). 62.0202 6.4E4 67.9397 3.2E4 68.9682 1.1E5 69.2105 3.4E4 71.0124 1.5E5 75.0073 3.0E5 77.7907 1.1E5 77.7958 1.7E5 78.9541 3.2E4 78.9577 2.7E5 85.0281 5.0E4 94.9350 4.0E4 96.1271 4.3E4 96.9683 3.6E5 99.0076 3.8E4 107.0354 4.1E4 111.0075 4.6E4 113.0230 4.3E4 123.8342 3.8E4 129.0177 4.6E4 134.0460 8.6E6 144.8176 4.0E4 150.3923 3.5E4 154.9975 1.0E5 237.0597 4.2E4 266.0893 7.6E4 282.7374 4.2E4 361.1140 4.9E4 461.6532 3.8E4 470.1525 1.0E5 496.1685 3.2E5 540.1572 3.7E5 558.1683 1.4E6 602.1586 3.0E5 638.1356 4.8E4 700.1361 4.1E6 END IONS