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 …

FragPipe Using FragPipe FragPipe can be downloaded here. Follow the instructions on that same Releases page to launch the program. Complete workflows are available for a variety of experiment …

Output files will depend on the workflow used and how experiments/groups are set on the ‘Workflow’ tab. This page lists the different output files generated by FragPipe. Main report files are either …

FragPipe Analyzing DIA data FragPipe can be downloaded here. Follow the instructions on that same Releases page to launch the program. See here for help configuring FragPipe. FragPipe currently …

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 …

FragPipe Label-free quantification with FragPipe This tutorial demonstrates label-free quantification with match-between-runs using a dataset published in Proteomics separates adult-type diffuse high …

FragPipe Open search for PTM discovery with FragPipe The open search strategy allows large mass differences between unmodified peptide sequences and experimentally observed precursors, …

FragPipe Glycoproteomics with FragPipe FragPipe has several workflows for analyzing LC-MS/MS data of intact glycopeptides that provide a variety of capabilities and options. Glyco searches use the …

A complete proteomics pipeline with the MSFragger search engine at heart

FragPipe TMT analyses with FragPipe FragPipe currently includes two tools for generating TMT quantification reports. For most workflows, it is recommended to use TMT-Integrator, which filters …