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

SIRIUS 6: no LC-MS chromatograms #157

Open JethroHemmann opened 3 weeks ago

JethroHemmann commented 3 weeks ago

Thanks for adding exciting new features to SIRIUS 6! :-)

When testing the new version with mzML files, I noticed that the LC-MS chromatogram is not working anymore and I just get empty plots. Is this a bug?

grafik

JethroHemmann commented 3 weeks ago

Ah, it works though when importing and aligning multiple files. But it used to work with a single file as well.

kaibioinfo commented 3 weeks ago

Hi, when importing single files there is no "preprocessing" going on. Instead, it just extracts all MS/MS from the file. It's quite important to import all the LCMS files at once to get a proper feature detection and isotope pattern extraction.

I have to think about if it makes sense to have a proper reworked "single file import".

JethroHemmann commented 3 weeks ago

Thanks for your response!

I often just load a single representative file to save some time, if I am just interested in a few specific metabolites. And in SIRIUS 5, the LC-MS tab also showed the peak in that case. So would be nice if that worked again in SIRIUS 6 :-)

typewritermonkey commented 3 weeks ago

Thanks for developing Sirius 6!

I also tried to do a test run with a single mzml file and had problems. Like not showing the chromatograms and not being able to filter out the bad ones before computing all lol. I just tried to import 3 mzmls at once and got this error message:

Error when importing data! Cause: java.lang.Exception: java.lang.IllegalArgumentException: Given retention time middle is not in range: 99.03114129675636 is not in [99.03114129675637, 103.02829512486207] java.lang.Exception: java.lang.IllegalArgumentException: Given retention time middle is not in range: 99.03114129675636 is not in [99.03114129675637, 103.02829512486207] at de.unijena.bioinf.ms.nightsky.sdk.jjobs.SseProgressJJob.updateAndCheckIfDone(SseProgressJJob.java:129) at de.unijena.bioinf.ms.nightsky.sdk.jjobs.SseProgressJJob$1.onNext(SseProgressJJob.java:76) at de.unijena.bioinf.ms.nightsky.sdk.jjobs.SseProgressJJob$1.onNext(SseProgressJJob.java:65) at de.unijena.bioinf.sse.FluxToFlowBroadcast.lambda$onNext$7(FluxToFlowBroadcast.java:103) at java.base/java.lang.Iterable.forEach(Unknown Source) at de.unijena.bioinf.sse.FluxToFlowBroadcast.onNext(FluxToFlowBroadcast.java:99) at de.unijena.bioinf.ms.nightsky.sdk.NightSkyClient.lambda$enableEventListening$3(NightSkyClient.java:198) at reactor.core.publisher.LambdaSubscriber.onNext(LambdaSubscriber.java:160) at reactor.core.publisher.FluxPublishOn$PublishOnSubscriber.runAsync(FluxPublishOn.java:446) at reactor.core.publisher.FluxPublishOn$PublishOnSubscriber.run(FluxPublishOn.java:533) at reactor.core.scheduler.WorkerTask.call(WorkerTask.java:84) at reactor.core.scheduler.WorkerTask.call(WorkerTask.java:37) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

kaibioinfo commented 3 weeks ago

Okay, that's definitely a bug. We will fix that with the next patch.