MRMAssayDB: a comprehensive integrated resource for targeted proteomics assays.

IF 2.8 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Expert Review of Proteomics Pub Date : 2025-09-18 DOI:10.1080/14789450.2025.2557023

Yassene Mohammed, Pallab Bhowmick, Christoph H Borchers

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引用次数: 0

Abstract

Introduction: Targeted quantitative proteomics is vital for accurate protein measurement in biological samples. Techniques like Multiple Reaction Monitoring (MRM or SRM) and Parallel Reaction Monitoring (PRM), often used with isotopically labeled internal standards, provide absolute quantification, and represent the current gold standard. However, developing and validating assays for individual proteins remains labor-intensive. Several repositories, such as CPTAC, SRMAtlas, PanoramaWeb, and PeptideTracker host targeted assay data with varying levels of detail. MRMAssayDB is an integrated platform that hosts and annotates the curated targeted proteomics assays from these resources.

Areas covered: First launched in 2018 and updated in 2021, the latest release of MRMAssayDB includes over 1.1 million assays for 939,000 peptides, enabling quantification of 61,000 proteins from 146 organisms. The database also maps proteins to 19,000 Gene Ontology terms and 4,000 biological pathways. A newly integrated visualization module projects peptide assays onto Alphafold-predicted 3D protein structures, allowing users to examine peptide locations, post-translational modifications, and disease mutations while also supporting mapping to structures in the Protein Data Bank (PDB).

Expert opinion: MRMAssayDB significantly improves access to validated proteotypic peptides and transition data, facilitating efficient assay selection and quantitative panel building for researchers in targeted proteomics. Availability: http://mrmassaydb2.proteomicscentre.com.

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MRMAssayDB：一个综合性的靶向蛋白质组学分析资源。

靶向定量蛋白质组学对生物样品中蛋白质的精确测量至关重要。多反应监测（MRM或SRM）和平行反应监测（PRM）等技术通常与同位素标记的内标一起使用，提供绝对定量并代表当前的金标准。然而，开发和验证单个蛋白质的检测方法仍然是劳动密集型的。几个存储库，如CPTAC， SRMAtlas， PanoramaWeb和PeptideTracker，以不同的详细程度托管目标分析数据。MRMAssayDB是一个集成平台，从这些资源中托管和注释精心策划的靶向蛋白质组学分析。MRMAssayDB于2018年首次推出，并于2021年更新，最新发布的MRMAssayDB包括对939,000个肽的超过110万次分析，能够量化来自146种生物的61,000种蛋白质。该数据库还将蛋白质映射到19,000个基因本体术语和4,000个生物途径。新集成的可视化模块将肽分析投影到alphafold预测的3D蛋白质结构上，允许用户检查肽位置，翻译后修饰和疾病突变，同时还支持到蛋白质数据库（PDB）中的结构映射。专家意见：MRMAssayDB显著改善了验证蛋白型肽和转换数据的获取，促进了靶向蛋白质组学研究人员高效的分析选择和定量小组的建立。可用性:http://mrmassaydb2.proteomicscentre.com。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Expert Review of Proteomics 生物-生化研究方法

CiteScore

7.60

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Expert Review of Proteomics (ISSN 1478-9450) seeks to collect together technologies, methods and discoveries from the field of proteomics to advance scientific understanding of the many varied roles protein expression plays in human health and disease. The journal coverage includes, but is not limited to, overviews of specific technological advances in the development of protein arrays, interaction maps, data archives and biological assays, performance of new technologies and prospects for future drug discovery. The journal adopts the unique Expert Review article format, offering a complete overview of current thinking in a key technology area, research or clinical practice, augmented by the following sections: Expert Opinion - a personal view on the most effective or promising strategies and a clear perspective of future prospects within a realistic timescale Article highlights - an executive summary cutting to the author''s most critical points.