@article{8754978,
  abstract     = {{In metaproteomics, the study of the collectiveproteome of microbial communities, the protein inference problemis more challenging than in single-species proteomics. Indeed, apeptide sequence can be present not only in multiple proteins orprotein isoforms of the same species, but also in homologousproteins from closely related species. To assign the taxonomy andfunctions of the microbial species, specialized tools have beendeveloped, such as Prophane. This tool, however, is not directlycompatible with post-processing tools such as Percolator. In thismanuscript we therefore presentPout2Prot, which takes PercolatorOutput (.pout)files from multiple experiments and creates proteingroup and protein subgroup outputfiles (.tsv) that can be useddirectly with Prophane. We investigated different groupingstrategies and compared existing protein grouping tools to develop an advanced protein grouping algorithm that offers a varietyof different approaches, allows grouping for multiplefiles, and uses a weighted spectral count for protein (sub)groups to reflectabundance.Pout2Protis available as a web application athttps://pout2prot.ugent.beand is installable via pip as a standalonecommand line tool and reusable software library. All code is open source under the Apache License 2.0 and is available athttps://github.com/compomics/pout2prot.}},
  author       = {{Schallert, Kay and Verschaffelt, Pieter and Mesuere, Bart and Benndorf, Dirk and Martens, Lennart and Van Den Bossche, Tim}},
  issn         = {{1535-3893}},
  journal      = {{JOURNAL OF PROTEOME RESEARCH}},
  keywords     = {{General Chemistry,Biochemistry,metaproteomics,computational proteomics,protein inference,bioinformatics,METAPROTEOMICS,INFERENCE,IDENTIFICATION}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{1175--1180}},
  title        = {{Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files}},
  url          = {{http://doi.org/10.1021/acs.jproteome.1c00685}},
  volume       = {{21}},
  year         = {{2022}},
}

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