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- Describe the issue or question:
I used FragPipe (17.1) to analyze 18 phospho-ddaPASEF files with MBR or without MBR to generate a spectral library.
In MBR search, I assigned all runs to the same e…
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# Description
I'm trying to run fragpipe on timsTOF Pro data for MSFragger database searches and IonQuant LFQ quantitation. I get an error at the PhilosopherFilter step.
I'm running on a Windows 1…
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Hello,
I'm attempting to run LFQ on a closed search of TIMSTOF DDA data, with the default IonQuant settings. I've run into an error at the Updating Philosopher's tables step, and unfortunately don't …
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com.javadeobfuscator.deobfuscator.executor.exceptions.NoSuchMethodHandlerException: Could not find invoker for java/lang/Object eoi/lfq/dy get(Ljava/lang/Object;)Ljava/lang/Object; @ store/supremesetu…
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### Description of bug
I have been running Philosopher 4.0.0 since August, and I was unable to reproduce a run that I had generated about a month ago due to
1. Philosopher not reading in the sp…
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Dear Nesvi lab, I'm sorry to bother you twice in 2 weeks. I have another problem.
Let me describe the workflow of my experiment:
1. Acquired short LC gradient (45 minutes) DIA data on a Thermo Q-E…
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I have ran the identification and LFQ pipeline with identity propagation between runs and now I want to export the results of:
1. database search within the search loop, so I get a separate csv for…
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Dear Matthias,
We obtain this error message. Do you have any idea what could be the problem.
Best, Peer
[1] "2021-10-05 17:29:45 Raw file conversion finished"
[1] "2021-10-05 18:32:01 Preparat…
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I searched two files generated from Bruker Impact II QTOF by loading the LFQ MBR search option. The problem is that I am not getting any intensity values in the output file, all the values are zero.
…
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Hi,
I just noticed an issue with the latest version of FragPipe (18.0): when I launch the GUI, I see that the PTMs tab is active and I can edit fields. PTM-Shepherd is set to active. As soon as I l…