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 am trying to run hybridDIA with 54 DIA folders and 57 DDA folders. I set a 3% FDR with group-specific FDR. I want to set the DDA folders...
- Describe the issue or question: Enabling writing sub-mzML fails with FragPipe v21 when the source MS data file is not an mzML file, but does work on v20. The...
- Describe the issue or question: I am trying to run diaumpire via fragpipe only but with it being the only tab checked in fragpipe, but it only runs check...
Hello, first I'll say thanks for the amazing software! I'm looking forward to trying DDA+ 😄 - Describe the issue or question: The default SILAC3 workflow (or likely any MS1...
Hello, Thank you for all the updates in the new FragPipe v21. I was curious to test out the new TMT Integrator version that uses IonQuant. Running the default TMT16...
I'm running MSFragger from the command line as part of a pipeline. I need away to control the **output directory** (I found only a parameter to control the output **format**...
Hi all! Is there a way to create a custom set of TMT tags? In general what we did, is to take the 16plex and divide it into two sets...
- Describe the issue or question: When will we be able to process PASEF data for TMT reporter ions?
Hello, we're studying organisms that has a general O-glycosylation system that targets a specific three amino acid motif. The regex for this motif would be `D[ST][AILVMTSGCF]` where it's the S...
Hi, We are running some data through DIA-SpecLib-Quant pipeline and we find that several peptides are quantified at wrong retention time (we check the chromatograms in Skyline) as shown in...
