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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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Empty .csv file while trying to use the FBMN export #139

Closed Socamibravo closed 10 months ago

Socamibravo commented 11 months ago

Hi! I have already computed all compounds (with masses <850Da) and was trying to export to GNPS so I can then use for my FBMN. I tried ticking and unticking the different options to see if it work, but in all cases, I only get correctly the .mgf file. The .csv file only contains the headers, no features inside. What i did was created a folder inside the Sirius option and then inside one file ending with the corresponding extensions. I attach the file I got as .CSV. If you know how to fix this, please let me know :) I´m using version 5.8.1. Btw, thank you for all the work you do! This version works quite faster :) Siriusoutput_c18cs_Round8_FractionE_filtered.csv

mfleisch commented 10 months ago

Hey, what is your initial input data format? Export of the quant table from SIRIUS does only work if you use mzml/mzxml as input because otherwise the quantitative information is not available anymore.

If you use an preprocessed format as input for SIRIUS (e.g. mgf exported from MZmine) you have to use the FBMN export from MZmine to create an input for FBMN.

If this answers your question please close the issue

Best Markus

Socamibravo commented 10 months ago

Hi mfleisch! Thank you very much for your answer! It was very informative. I used a file from MzMine3 (processed, .mgf). Sorry, when I tried to explain it was late in the afternoon and I was quite tired. Thank you, Sofia