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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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Negative ionization mode interpretation in Sirius MS format #57

Closed AharoniLab closed 2 years ago

AharoniLab commented 2 years ago

Hi. I see a possible bug in the reading/interpretation of MS files with unknown adduct in the negative ionization mode. E.g. for the following input:

_

compound 100008992 (1-stearoyl-2-docosahexaenoyl-GPE) parentmass 790.5395 ionization [M-?]- instrumentation Waters QTOF-HRMS

ms1 790.5405827917 523.65971971618 791.544290518561 273.425397221785 792.551573367295 52.3557014903044

ms2 165.0403 14242.8135 239.0586 2731.761 239.2387 142.4587 253.2161 2793.1611 269.2481 18269.2871 270.2509 1593.8157 etc. _

Sirius-4.9.5-win64 CLI automatically generates the following .ms file: _

compound 100008992 (1-stearoyl-2-docosahexaenoyl-GPE) parentmass 790.5395 ionization [M]- instrumentation Q-ToF (LCMS) source [local path the original .ms file] quality UNKNOWN

ms1peaks 790.5405827917 523.65971971618 791.544290518561 273.425397221785 792.551573367295 52.3557014903044

ms2peaks etc. _

By converting the adduct from unknown to a naturally deprotonated ion, Sirius creates a downstream error in neutral formula calculation which further results in missing or wrong CSI-FID annotation etc. By manually fixing the [M]- to [M-H]- I could restore the correct formula and further get some nice annotations by CSI and CANOPUS. However as I see that this is a reoccurring pattern for all [M+?]- tags, which does not happen in the positive mode - where [M+?]+ tags remain as such - I think there is sufficient reason to open a bug report.

marcus-ludwig commented 2 years ago

Hi,

the generic unknown negative ionization is specified as [M+?]- in SIRIUS. If you use [M-?]- this will be incorrectly recognized and parsed to [M]-. But [M+?]- should work fine.

Best, Marcus