FragPipe | A complete proteomics pipeline with the MSFragger search ...
FragPipe is a comprehensive computational platform designed for the analysis of mass spectrometry-based proteomics data. It includes a Graphical User Interface and pipeline wrapper code (FragPipe …
Using FragPipe
Connect FragPipe to a MSFragger.jar, IonQuant.jar, and diaTracer.jar program files. If you already have the latest versions and they are in the same folder, use the ‘Browse’ button to select the folder.
FragPipe workflows
FragPipe FragPipe workflows Listed below are the analysis workflows provided with FragPipe. Workflows can be customized and saved (with a unique name) for later use. Visit workflow sharing to …
Analyzing DIA data | FragPipe
The files can be downloaded from here. Configure FragPipe Python (with EasyPQP installed) is needed for spectral library generation. On the Config tab, check that a valid Python path is provided (Python …
Guide to FragPipe results
This page lists the different output files generated by FragPipe. Main report files are either comma-separated (csv) or tab-separated (tsv), and their column contents are described here.
Label-free quantification with FragPipe
When you launch FragPipe, check that MSFragger, IonQuant, and Philosopher are configured. (If you haven’t downloaded them yet, use their respective ‘Download / Update’ buttons.
Setting up FragPipe
FragPipe and MSFragger both require a 64-bit OpenJDK to run. Windows users can choose to download the -jre- version of FragPipe (see below) or install 64-bit pre-built OpenJDK here.
Glycoproteomics with FragPipe
When you launch FragPipe, check that MSFragger and Philosopher are both configured. If you haven’t downloaded them yet, use their respective ‘Download / Update’ buttons.
Open search for PTM discovery with FragPipe
Mar 14, 2014 · One of the benefits of FragPipe is that unknown mass shifts can be easily incorporated without knowing their identities. This mass shift is strongly localized to R and moderately localized to E.
TMT analyses with FragPipe
Find the fragpipe folder and open the fragpipe/bin subfolder. Double-click the fragpipe.exe file on Windows (or the fragpipe file on Linux) to launch the FragPipe program.