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
I am evaluating the accuracy of Fragpipe. Using Fragpipe 19.1 (MSFragger-3.7; IonQuant-1.8.10; philosopher_v4.8.0; Percolator 3.05), I run an LFQ analysis on publicly available data. I used files six files (...
Hi all, Thank you for your continuing work on MSFragger! After the re-introduction of .mgf files in 3.7, I ran into a new problem with uploading files into Skyline: While...
Hello, When running FragPipe on my TMT data, I noticed that it only gives one NumberPSM column when I have two or three TMT plexes. How do I tell how...
Dear Fragpipe Team, thanks for your amazing work! We are currently trying to extract information at fragment ion level from FragPipe results. Ideally, we would need a report file that...
Dear developers, would it be feasible to report the normalized as well as the non-normalized intensities of proteins/peptides etc in the result tables? Currently there is only the intensity column...
Dear developers, would it be feasible to include unique row identifiers which link information in the various combined_* results tables? This way one could look up relatively easily connected information...