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
Subject
Molecular Biology,Biochemistry
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献