Proteogenomics peptide identification

[bibshow file=2016_2.bib] This TOPPAS workflow implements peptide identification and filtering, suitable for finding novel peptides to help improve genome annotations. [bibcite key=weisser2016flexible] Prerequisites: On the software side, the workflow requires OpenMS 2.0.1, the database search engines MS-GF+ and Mascot, as well as the post-processing tools Percolator and Mascot Percolator. On the data side, suitable tandem [...]

iTRAQ quantitation and identification

This page describes an iTRAQ quantitation and identification workflow. Assumptions: You have recorded iTRAQ data in HCD/CID mode on an Orbitrap hybrid instrument. What it does: Peptide quantitation using the ITRAQAnalyzer tool and FDR-controlled identification using three different search engines, which HCD and CID spectra searched separately (for better FDR). How to run it: Install [...]