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Computational approaches to identify sites of phosphorylation.

التفاصيل البيبلوغرافية
العنوان: Computational approaches to identify sites of phosphorylation.
المؤلفون: Joyce AW; Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA.; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA., Searle BC; Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA.; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA.
المصدر: Proteomics [Proteomics] 2024 Apr; Vol. 24 (8), pp. e2300088. Date of Electronic Publication: 2023 Dec 24.
نوع المنشور: Journal Article; Review
اللغة: English
بيانات الدورية: Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101092707 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1615-9861 (Electronic) Linking ISSN: 16159853 NLM ISO Abbreviation: Proteomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Weinheim, Germany : Wiley-VCH,
مواضيع طبية MeSH: Algorithms* , Search Engine*, Phosphorylation ; Mass Spectrometry/methods ; Phosphopeptides/metabolism
مستخلص: 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.
(© 2023 The Authors. PROTEOMICS published by Wiley‐VCH GmbH.)
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معلومات مُعتمدة: R35 GM150723 United States GM NIGMS NIH HHS; R01GM133981 United States GM NIGMS NIH HHS; R21CA267394 United States NH NIH HHS; R35GM150723 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: bioinformatics; mass spectrometry; phosphoproteomics
المشرفين على المادة: 0 (Phosphopeptides)
تواريخ الأحداث: Date Created: 20231028 Date Completed: 20240418 Latest Revision: 20240617
رمز التحديث: 20240617
DOI: 10.1002/pmic.202300088
PMID: 37897210
قاعدة البيانات: MEDLINE
الوصف
تدمد:1615-9861
DOI:10.1002/pmic.202300088