BayesENproteomics: Bayesian Elastic Nets for Quantification of Peptidoforms in Complex Samples

Venkatesh Mallikarjun, Stephen M Richardson, Joe Swift

Research output: Contribution to journalArticlepeer-review


Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behavior of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in the levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.

Original languageEnglish
Pages (from-to)2167-2184
Number of pages18
JournalJournal of Proteome Research
Issue number6
Publication statusPublished - 5 Jun 2020


  • Bayes Theorem
  • Humans
  • Peptides/metabolism
  • Protein Processing, Post-Translational
  • Proteomics
  • Tandem Mass Spectrometry


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