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I'm currently running Philosopher on Linux via my universities Linux HPC Cluster
I'm having problems of getting the rest of the Philosopher workflow to work on my MSFragger output (I used the scri…
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Hello,
I am having trouble running a pipeline without ProteinProphet in Philosopher. The problem seems to be that I have turned off ProteinProphet in the config file, but when it gets to the filter…
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[log_2020-03-12_15-04-52.txt](https://github.com/Nesvilab/FragPipe/files/4323725/log_2020-03-12_15-04-52.txt)
**Describe the bug**
I am trying to run mzxml files on fragpipe to get mass spec data …
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Hi,
I am trying to analyze the proteomics data from tims tof pro.
I have used *.mgf files to run in MS fragger (both with fragpipe and proteome discoverer node)
Both of them failed to read the …
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Greetings,
The following error occurs during SpecLibGen of the DIA-U track in FragPipe.
SpecLibGen [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
C:\ProgramData\Anaconda3\py…
sjr24 updated
3 years ago
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I seem to get consistently lower protein ID rates (20% less, considering proteins with at least 1 unique peptide) and peptide IDs (40% less, 1% FDR) using the philosopher TMT pipeline described in th…
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Dear all,
Please, I am a beginner using MSFRagger, and I have some doubts about it.
First, I have some TMT data to analyze. However, there is no reference channel.
Should I set the reference c…
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I have copied the error that I am repeatedly facing with MSfragger -glyco
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_251, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
…
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Dear Felipe,
using the philosopher 1.5.1 the following error code occurs when I try to filter SpectraST search results:
Cannot decode packed binary. strconv.ParseFloat: parsing "Normal": invalid…
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Hi,
I run MSFragger 3.1.1 on linux system with calibrate_mass = 2. it calibrate the masses but didn't find any optimal parameters. when I run MSFragger through FragPipe on the same database with sam…