Candida albicans: A Comprehensive View of the Proteome.

IF 3.6 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-14 DOI:10.1021/acs.jproteome.4c01020

Leticia Gomez-Artiguez, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, Lucía Monteoliva, Robert L Moritz, Eric W Deutsch, Concha Gil

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Abstract

We describe a new release of the Candida albicans PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The C. albicans PeptideAtlas summary web page provides "Build overview", "PTM coverage", "Experiment contribution", and "Data set contribution" information. The protein and peptide information can also be accessed via the Candida Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments that identify each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyze PTM results is provided in the PeptideAtlas of this important pathogen. Candida albicans PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578.

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白色念珠菌：蛋白质组学的综合观点。

我们描述了一个新发布的白色念珠菌PeptideAtlas蛋白质组学光谱资源（构建2024-03），在典型蛋白水平上提供79.5%的序列覆盖率，匹配的质谱，以及实验证据，鉴定出3382和536个磷酸化丝氨酸和苏氨酸位点，错误定位率分别为1%和5.3%。我们提供了一个关于如何使用PeptideAtlas和相关工具来访问这些信息的教程。白色念珠菌肽图谱摘要网页提供“构建概述”、“PTM覆盖范围”、“实验贡献”和“数据集贡献”信息。蛋白质和肽信息也可以通过每个蛋白质页面上的超链接通过念珠菌基因组数据库访问。这允许用户仔细研究鉴定的肽，蛋白质覆盖，翻译后修饰（PTMs），以及鉴定每种蛋白质的实验。鉴于了解每个蛋白质序列中PTM景观的价值，如何解释和分析PTM结果在这种重要病原体的肽图谱中提供了更详细的解释。白色念珠菌肽图谱网页：https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578。

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来源期刊

Journal of Proteome Research 生物-生化研究方法

CiteScore

9.00

自引率

4.50%

发文量

251

审稿时长

3 months

期刊介绍： Journal of Proteome Research publishes content encompassing all aspects of global protein analysis and function, including the dynamic aspects of genomics, spatio-temporal proteomics, metabonomics and metabolomics, clinical and agricultural proteomics, as well as advances in methodology including bioinformatics. The theme and emphasis is on a multidisciplinary approach to the life sciences through the synergy between the different types of "omics".