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Hello,
My question is in the title. Here are more details:
I generated a spectral library with Fragpipe using unspecific digestion (immunopeptidomics data). I then would like to match this librar…
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### PXD001819 Analysis
Currently, we have a workflow that can perform peptide identification using: `-> ms2rescore -> SNR + spectrum properties -> percolator`
Here the results can be found (http…
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Dear Mrs
Thanks for your work of MSGF+, it is really an wonderful search engine. But I encountered confusion in the data format used for searching. I used MSGF+ in immunopeptidomics, at first, I co…
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Many papers on mass-spectrometry based proteomics have shown the use of deep learning for intensity prediction, combining scores across search algorithms, retention time, collision corss section predi…
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**- 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 truncation, then attach the…
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[log_2024-06-12_12-37-59.txt](https://github.com/user-attachments/files/15806888/log_2024-06-12_12-37-59.txt)
**Hi, I've been using FragPipe for many of my large scale proteomics and immunopeptidom…
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Hi,
Where can I change the enzyme parameters in the GUI application for peptidomics data? I've tried to input in the Mokapot FASTA parameters the Enzyme as '.' (as written in the Mokapot documentat…
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Thank you for publishing this fanastic resource for immunopeptidomics. I recently started looking through your work, but today found that the website (https://systemhc.sjtu.edu.cn/) is returning a 403…
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Dear MSFragger team,
I encountered an error when trying to use FragPipe to search a timsTOF DDA dataset for immunopeptidomics, as follows:
**Loading predicted spectra
Process 'MSBooster' fini…
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[log_2024-06-06_18-51-57_Bjoren_AB_run1-25_06062024_test01.txt](https://github.com/user-attachments/files/15688923/log_2024-06-06_18-51-57_Bjoren_AB_run1-25_06062024_test01.txt)
Dear MSFragger te…