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
Dear developers! In our TMTPro-16plex labeling data, 126 and 134N channels without peptides, other channels labeled with HEK and HeLa peptide. in this case, we found more than 5% of...
 Hello, developer! i ran fragpipe and got above error msg. do you have any idea? -detail info- ubuntu 22.04 LTS MSFragger 3.5 IonQuant 1.8.0 Philosopher 4.4.0 python 3.9.12
Hello MSFrager Team, I have been trying to analyze my glycoproteomic data (orbitrap) with MSFrager as the identifications and their confidence looks better than other search engines. But I am...
Dear MSFragger team, Thanks for developing this nice piece of software! I'm looking into two modifications in the same LC-MS/MS run and I know they have specific diagnostic ions and...
- Describe the issue or question: Hi, FragPipe Team I've got the error message of "panic: runtime error: index out of range [1] with length 0" at the DBAnnotate stage...
### Context I'm making my first steps with the _LFQ-MBR_ workflow in order to compare its performance with other search soft. Since I like to have Proteins and PSMs information...
Dear Fengchao/Alexey, is there actually a way to extract information on which spectra were actually considered for TMTintegrator-based quan? This information would be highly useful in individual cases (i.e. which...
Hello, While trying to run LFQ-phospho the following error was encountered: ERRO[19:13:18] Cannot decode packed binary. XML syntax error on line 2076829: unexpected EOF I may have seen a similar...
I'm trying to run a phospho-LFQ workflow, and I'm having the following error: - panic: Cannot decode packed binary. XML syntax error on line 104220: unexpected EOF; and - ERRO[23:25:48]...
I tried to use LFQ-phopho workflow to quantify my phosphoproteomics data. I converted the raw files into mzML files, and run the workflow in FragPipe (v 18.0). However, it showed...
