Computational approaches to identify sites of phosphorylation

Author:

Joyce Alex W.12,Searle Brian C.123ORCID

Affiliation:

1. Department of Biomedical Informatics The Ohio State University Medical Center Columbus Ohio USA

2. Pelotonia Institute for Immuno‐Oncology The Ohio State University Comprehensive Cancer Center Columbus Ohio USA

3. Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA

Abstract

AbstractDue 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.

Funder

National Institutes of Health

National Institute of General Medical Sciences

Publisher

Wiley

Subject

Molecular Biology,Biochemistry

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