search

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
78 stars 17 forks source link

Input .mzXML file, but nothing happened, formular annotation on "MS1 only" supported? #34

Closed xxing9703 closed 3 years ago

xxing9703 commented 3 years ago

I tried to load my .mzXML Data in Sirius, but no peak list was shown on the left side. LC-MS .raw data was taken on QE, consisting of MS1 scan only, and was converted to .mzXML by ProteoWizard. I'm wondering if Sirius can annotate MS1 data without fragmentation info provided? and is this (MS1 only) the cause of the problem (not loaded successfully)?

mfleisch commented 3 years ago

Hey, yes we currently do not support MS1 only data and this is also the reason why the import fails. You should see the messages that explain why your data was not imported in the log window.

We will support this in the future in the command line tool. Support in the GUI might be possible but needs to be discussed. I will post updates here.

xxing9703 commented 3 years ago

Hi Markus: Thanks very much for your quick reply. We also did MS2 on some of the manually selected features from the MS1 run, and converted into mzXML files. I tried and however they cannot be loaded successfully either. Is it because they are not data dependent MS2? If I want to use Sirius/Zodiac to perform formula annotations of these selected peaks, how do I need to prepare/convert the data into the right input format?

mfleisch commented 3 years ago

Could you post the output of the Log window? A common problem is that the input data is profile and not centroided data.

Have you already seen these tutorials? https://www.youtube.com/playlist?list=PL57Jv_39fTdc_j8eHrH6At81n1AtxeKar

xxing9703 commented 3 years ago

Yes, the log says its not centroided data. I used Rawconverter to convert the MS2 data into mzXML, maybe some settings are not correct. Now, I use MSconvert to convert the data and it works.