Computational approaches to identify sites of phosphorylation
- Alex Joyce,
- Brian Searle
Abstract
Due to their oftentimes ambiguous nature, phosphopeptide positional
isomers can present challenges in bottom-up mass spectrometry-based
workflows as search engine scores alone are often not enough to
confidently distinguish them. Additional scoring algorithms can remedy
this by providing confidence metrics in addition to these search
results, reducing ambiguity. Here we describe challenges to interpreting
phosphoproteomics data and review several different approaches to
determine sites of phosphorylation for both data-dependent and
data-independent acquisition-based workflows. Finally, we discuss open
questions regarding neutral losses, gas-phase rearrangement, and false
localization rate estimation experienced by both types of acquisition
workflows and best practices for managing ambiguity in phosphosite
determination.15 Jun 2023Submitted to PROTEOMICS 15 Jun 2023Review(s) Completed, Editorial Evaluation Pending
15 Jun 2023Submission Checks Completed
15 Jun 2023Assigned to Editor
15 Jun 2023Reviewer(s) Assigned
09 Aug 2023Editorial Decision: Revise Minor
07 Oct 2023Review(s) Completed, Editorial Evaluation Pending
07 Oct 20231st Revision Received
09 Oct 2023Editorial Decision: Accept