protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data.

Autor: Quast JP; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland., Schuster D; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland.; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland., Picotti P; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.
Jazyk: angličtina
Zdroj: Bioinformatics advances [Bioinform Adv] 2021 Dec 10; Vol. 2 (1), pp. vbab041. Date of Electronic Publication: 2021 Dec 10 (Print Publication: 2022).
DOI: 10.1093/bioadv/vbab041
Abstrakt: Summary: We present a flexible, user-friendly R package called protti for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format.
Availability and Implementation: protti is implemented as an open-source R package. Release versions are available via CRAN (https://CRAN.R-project.org/package=protti) and work on all major operating systems. The development version is maintained on GitHub (https://github.com/jpquast/protti). Full documentation including examples is provided in the form of vignettes on our package website (jpquast.github.io/protti/).
(© The Author(s) 2021. Published by Oxford University Press.)
Databáze: MEDLINE
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