Computational approaches to identify sites of phosphorylation

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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.

Location: Deutsche Nationalbibliothek Frankfurt am Main

Extent: Online-Ressource

Language: Englisch

Bibliographic citation: Computational approaches to identify sites of phosphorylation ; day:24 ; month:12 ; year:2023 ; extent:14
Proteomics ; (24.12.2023) (gesamt 14)

Creator: Joyce, Alex W.
Searle, Brian C.

DOI: 10.1002/pmic.202300088

URN: urn:nbn:de:101:1-2023122514063211839151

Rights: Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.

Last update: 15.08.2025, 7:30 AM CEST

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Joyce, Alex W.
Searle, Brian C.

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Computational approaches to identify sites of phosphorylation

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Other Objects (12)

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