FragPipe
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Nesvilab
A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
Hi there, I was running Diagnostic ion mining workflow that finished with the following message: > Identifying candidate ions > Building feature histograms > Exception in thread "main" java.lang.NullPointerException >...
Hi, I am quite new to MSFragger. I searched an LFQ dataset, and I would like to remove proteins identified by 1 razor+unique peptide in the combined_protein file, however I...
Greetings, I am not sure if this is currently possible, but it would be great to allow MSFragger-Glyco (N-linked workflows) to assign glycans to peptides with a motif that is...
**- Upload your log file** [log_2024-05-10_14-52-03-ModTag.txt](https://github.com/Nesvilab/FragPipe/files/15279003/log_2024-05-10_14-52-03-ModTag.txt) [log_2024-05-10_15-01-17-none.txt](https://github.com/Nesvilab/FragPipe/files/15279006/log_2024-05-10_15-01-17-none.txt) **- Describe the issue or question:** Hello, I found that while the TMT Integrator in my workflow runs successfully, the generated report is...
Dear Fragpipe team, I encountered an error while using Fragpipe in the process of mass calibration and parameter optimization. *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1...
Hi, I am trying to process parallel DDA/DIA files through FragPipe using the glyco-DIA workflow. It is generating a DIA-NN output but not a Skyline document. Thanks, Matt [log_2024-10-10_10-24-06.txt](https://github.com/user-attachments/files/17330199/log_2024-10-10_10-24-06.txt)
I've been trying to run the DIA_SpecLib_Quant_Phospho_diaPASEF workflow, and I keep getting a non-zero exit code (137) in diaTracer that cancels the workflow. I've attached the log. I'm happy to...
[log_2024-10-25_16-14-59.txt](https://github.com/user-attachments/files/17543641/log_2024-10-25_16-14-59.txt) **- Upload your log file** (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid...
Hi, I am running MS Fragger with a modified standard TMT workflow, though I need MS fragger to do a semi-tryptic search Unfortunately it stops at TMT Intergrator. "For input...
Hi all, I'm having a similar proplem to that deatiled in this [thread ](https://github.com/Nesvilab/FragPipe/issues/152) so I thought I'd open up a new issue. I double-checked and I didn't have any...
