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Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files

Tim Van Den Bossche (UGent) , Kay Schallert, Pieter Verschaffelt (UGent) , Bart Mesuere (UGent) , Dirk Benndorf and Lennart Martens (UGent)
(2021) BIORXIV.
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Abstract
The protein inference problem is complicated in metaproteomics due to the presence of homologous proteins from closely related species. Nevertheless, this process is vital to assign taxonomy and functions to identified proteins of microbial species, a task for which specialized tools such as Prophane have been developed. We here present Pout2Prot, which takes Percolator Output (.pout) files from multiple experiments and creates protein (sub)group output files (.tsv) that can be used directly with Prophane. Pout2Prot offers different grouping strategies, allows distinction between sample categories and replicates for multiple files, and uses a weighted spectral count for protein (sub)groups to reflect (sub)group abundance. Pout2Prot is available as a web application at https://pout2prot.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the Apache License 2.0 and is available at https://github.com/compomics/pout2prot.

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MLA
Van Den Bossche, Tim, et al. “Pout2Prot : An Efficient Tool to Create Protein (Sub)Groups from Percolator Output Files.” BIORXIV, no. 11/08/2021, 2021, doi:10.1101/2021.08.11.455803.
APA
Van Den Bossche, T., Schallert, K., Verschaffelt, P., Mesuere, B., Benndorf, D., & Martens, L. (2021). Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files. https://doi.org/10.1101/2021.08.11.455803
Chicago author-date
Van Den Bossche, Tim, Kay Schallert, Pieter Verschaffelt, Bart Mesuere, Dirk Benndorf, and Lennart Martens. 2021. “Pout2Prot : An Efficient Tool to Create Protein (Sub)Groups from Percolator Output Files.” BIORXIV. https://doi.org/10.1101/2021.08.11.455803.
Chicago author-date (all authors)
Van Den Bossche, Tim, Kay Schallert, Pieter Verschaffelt, Bart Mesuere, Dirk Benndorf, and Lennart Martens. 2021. “Pout2Prot : An Efficient Tool to Create Protein (Sub)Groups from Percolator Output Files.” BIORXIV. doi:10.1101/2021.08.11.455803.
Vancouver
1.
Van Den Bossche T, Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L. Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files. BIORXIV. 2021.
IEEE
[1]
T. Van Den Bossche, K. Schallert, P. Verschaffelt, B. Mesuere, D. Benndorf, and L. Martens, “Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files,” BIORXIV, no. 11/08/2021. 2021.
@misc{8727336,
  abstract     = {{The protein inference problem is complicated in metaproteomics due to the presence of homologous proteins from closely related species. Nevertheless, this process is vital to assign taxonomy and functions to identified proteins of microbial species, a task for which specialized tools such as Prophane have been developed. We here present Pout2Prot, which takes Percolator Output (.pout) files from multiple experiments and creates protein (sub)group output files (.tsv) that can be used directly with Prophane. Pout2Prot offers different grouping strategies, allows distinction between sample categories and replicates for multiple files, and uses a weighted spectral count for protein (sub)groups to reflect (sub)group abundance.

Pout2Prot is available as a web application at https://pout2prot.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the Apache License 2.0 and is available at https://github.com/compomics/pout2prot.}},
  author       = {{Van Den Bossche, Tim and Schallert, Kay and Verschaffelt, Pieter and Mesuere, Bart and Benndorf, Dirk and Martens, Lennart}},
  language     = {{eng}},
  number       = {{11/08/2021}},
  series       = {{BIORXIV}},
  title        = {{Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files}},
  url          = {{http://doi.org/10.1101/2021.08.11.455803}},
  year         = {{2021}},
}
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