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 Fragpipe team, FYI - in the dabase section, if you use a fasta file with the proteome of e.g. rabbit and use the function "add contaminants and decoys", some...
- Describe the issue or question: Hello, We are trying to run a sizeable data set (64 .raw files, 143GB), I am trying it on Amazon Cloud at 64Gb RAM....
Hi, I got the following error "ERRO[08:36:50] Cannot decode packed binary. XML syntax error on line 3631: unexpected EOF", and fragpipe stopped. I have attached the whole log file for...
Added ability to change search engine to Comet: - Comet params have to be specified via parameter file, no UI - Did not add support for headless mode - Only...
- Describe the issue or question: Hello, I am struggling with an issue with FragPipe v16.0 while quantifies PSMs in TMT-10 dataset. It seems the tool is not able to...
Dear Fragpipe team, As always, many thanks for the amazing work you do developing maintaining Fragpipe and all its tools. Would it be possible to offer intensity grouping by modified...
- Describe the issue or question: Hi, I am importing a dataset into skyline using the pep.xml files following the tutorial and I don't understand why peptides that are not...
- Describe the issue or question: After saving a workflow in FragPipe, the selection drop-down defaults back to the first workflow on the list. This is confusing and may cause...
Dear FragPipe team, I'm using FragPipe 18.0 to process some DDA data to generate spectral library, and found some peptides that are not in the digestion rule of stricttrypsin appeared...
Is there a way to analyze SILAC samples including match-between runs with FragPipe? Thanks in advance! Michael
