openswathidpicker 0.0.5

A protein inference package used for OpenSWATH data

IDpicker for OpenSWATH

This is a package that is an implementation of a protein inference algorithm called IDpicker[1]. It is an algorithm that reads a protein-peptide mapping as graph, merges protein that map to an identical set of peptides, separate the graph into components, then greedily choose the protein that corresponds to most peptide for each component, until all peptides are covered by a chosen protein.

This implementation can only read the output of openSWATH [2]. The advantage of this algorithm compare to other ones for openSWATH is that, this one can handle peptide that map to multiple proteins.

There is only 1 function (just 'main') for this package with options on input_file path, q_limit_pep, context, run_id

main(input_file: str, q_limit_pep: str, context: str, run_id: str)

input_file is a path to the osw file

q_limit_pep is a number represent the maximum qvalue the user wants

context is either 'global' or 'run-specific'

run_id is either the id of the run that user want to use, or if the context is global, it can be anything, it will not be used.

We strongly advice to install PyProphet in a Python virtualenv.

citations

1. Zhang, B., Chambers, M. C., & Tabb, D. L. (2007). Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Journal of proteome research, 6(9), 3549–3557. https://doi.org/10.1021/pr070230d
2. Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L., Miladinović, S. M., Schubert, O. T., Wolski, W., Collins, B. C., Malmström, J., Malmström, L., & Aebersold, R. (2014). OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature biotechnology, 32(3), 219–223. https://doi.org/10.1038/nbt.2841