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

• Published in: Bioinformatics advances Vol. 2; no. 1; p. vbab041
• Main Authors: Quast, Jan-Philipp, Schuster, Dina, Picotti, Paola
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2022
• Subjects: Application Note; Mass spectroscopy; Proteolysis; Proteomes; Proteomics; Quality control
• ISSN: 2635-0041; 2635-0041
• DOI: 10.1093/bioadv/vbab041

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/).