<![CDATA[BOL: ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis]]> https://bioinformaticsonline.com/bookmarks/view/41475/proteoclade-a-taxonomic-toolkit-for-multi-species-and-metaproteomic-analysis? https://bioinformaticsonline.com/bookmarks/view/41475/proteoclade-a-taxonomic-toolkit-for-multi-species-and-metaproteomic-analysis Wed, 18 Mar 2020 14:27:20 -0500 https://bioinformaticsonline.com/bookmarks/view/41475/proteoclade-a-taxonomic-toolkit-for-multi-species-and-metaproteomic-analysis <![CDATA[ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis]]> ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements.

ProteoClade helps you analyze two general categories of experiments:

  1. Targeted Database Searches: Experiments in which a limited number of species are defined ahead of time, such as those involving Patient-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence databases are used for targeted searches (ex: using Mascot, MaxQuant).

  2. De Novo Searches: Experiments in which the organisms are unspecified ahead of time or involve samples of high taxonomic complexity. Mass spectra are analyzed in the absence of a reference database (ex: using PEAKS, PepNovo).

ProteoClade scales from two organisms to every organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741

Address of the bookmark: https://github.com/HeldLab/ProteoClade

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