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- I've been using the fragpipe N-Glyco-HCD/LFQ and O-Glyco-HCD workflows for glycopeptide analysis. Some of my protocols involve chemical modifications to terminal glycans. I am wondering if there is a...
Hi, We are performing glycopeptide identification and quantification across many samples. The data in the "assigned modifications" column of the "combined_modified_peptide.tsv" file gives only the mass of the glycan, not...
- Describe the issue or question: Hi, do you plan to support MSFragger-DIA for Bruker TimsTOF files? is it on your development roadmap? thanks Assaf - Upload your log file...
- Describe the issue or question: I wanted to ask if there is a way to generate the total ion current (TIC) vs retention time for any peptide from the...
Hi all, I was wondering if it is possible to save presets in PDV. I was looking at the documentation but could not find anything relevant (maybe my Google-Fu isn't...
Hi, Thanks again for developing these excellent tools. I'm analysing dimethyl-labelled samples, and I'm running into issues with search space + some incorrect PSMs. Perhaps this is addressed by another...
Dear developers, **Describe the issue or question** I found an old issue [#396](https://github.com/Nesvilab/FragPipe/issues/396) were you said that you will discuss internally if you add multiple fasta support to FragPipe. I...
Dear FragPipe Team, **Is your feature request related to a problem?** The request is not directly related to a problem but it would allow using the FragPipe outputs for additional...
Dear FragPipe team, I am currently processing some phophoenrichment samples using FragPipe. I was wondering whether there is not only the option to filter out modified peptides for protein quantification...
Sorry to bother you again Fengchao. I really like using MSstats and really appreciate the msstats output file you have fragpipe generate. I've seen in the past people have asked...
