This TOPPAS workflow implements peptide identification and filtering, suitable for finding novel peptides to help improve genome annotations. [1]

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 mass spectrometry data and sequence databases need to be provided.

See the description in the workflow for detailed information about inputs, output and parameters.

References:

[1] [doi] H. Weisser, J. C. Wright, J. M. Mudge, P. Gutenbrunner, and J. S. Choudhary, “Flexible Data Analysis Pipeline for High-Confidence Proteogenomics,” Journal of Proteome Research, vol. 15, iss. 12, pp. 4686-4695, 2016.
[Bibtex]
@article{weisser2016flexible,
title={Flexible Data Analysis Pipeline for High-Confidence Proteogenomics},
author={Weisser, Hendrik and Wright, James C and Mudge, Jonathan M and Gutenbrunner, Petra and Choudhary, Jyoti S},
journal={Journal of Proteome Research},
volume={15},
number={12},
pages={4686--4695},
year={2016},
publisher={ACS Publications},
doi={10.1021/acs.jproteome.6b00765}
}