NovoBridge (plus) | De novo metaproteomics pipeline

This is the repository for the NovoBridge pipeline, as described in:
Hugo B. C. Kleikamp, Mario Pronk, Claudia Tugui, Leonor Guedes da Silva, Ben Abbas, Yue Mei Lin, Mark C.M. van Loosdrecht and Martin Pabst* Database-independent de novo metaproteomics of complex microbial communities, Cell Systems (2021) doi:10.1016/j.cels.2021.04.003

The pipeline was established and tested with shotgun (meta)proteomics data obtained from Q Exactive Orbitrap Mass Spectrometers, using either PEAKS or DeepNovo generated de novo sequence lists. The generation of accurate de novo peptide sequence lists depends on high quality peptide sequencing spectra.

NovoBridge has been tested only in an Anaconda Spyder environment!
Novobridge + is essentially the same pipeline as Novobridge, with two modifications:

Tryptic digestion of uncleaved peptides: Since uncleaved peptides do not give an exact match with unipept API, each uncleaved peptide is cleaved and its peptides are submitted seperately.
Multiple candidate submission: Since both PEAKs and Deepnovo can have mutiple good scoring candidate peptides for a single spectra, subsequent submission of candidate peptides is performed to increase recall.

What is Novobridge?
Novobridge is an automated pipeline for fast processing, and integrated annotation and visualization of de novo proteomics data.