PaxDb v6.0:重新处理,LLM选择,精选的跨生物体蛋白质丰度数据
Qingyao Huang1,2, Damian Szklarczyk1,2, John Oehninger2
1Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
Nucleic acids research
|November 3, 2025
概括
PaxDb v6.0 数据库为392个物种提供了标准化的蛋白质丰度参考,提高了质谱 (MS) 实验的可重复性和数据重复使用. 该资源通过将重新处理的公共MS数据与一致的元数据集成,增强了生物洞察力.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 生物信息学是一种生物信息学.
- 系统生物学 系统生物学
背景情况:
- 质谱 (MS) 数据的重复使用受到不一致的处理和元数据的阻碍,限制了生物发现.
- 标准化,高覆盖度的参考资源对于蛋白质组学中的可复制性和跨研究整合至关重要.
- PaxDb为健康的野生类型状态提供了生物体和组织水平的蛋白质丰度数据.
研究的目的:
- 以更新和扩展的蛋白质丰度数据来增强PaxDb数据库.
- 开发一种标准化,自动化的管道,用于重新处理公共质谱数据.
- 提高公共蛋白质组学数据的可访问性和实用性,用于生物研究.
主要方法:
- 将来自 392 个物种的 1639 个数据集集集成到 PaxDb v6.0.0. 中.
- 开发了一个端到端的MS数据处理管道,使用FragPipe框架进行一致的再分析.
- 实现了标准化的元数据集成,正义映射和质量评分.
- 利用大型语言模型集合分类器进行半自动化策划ProteomeXchange项目.
- 创建了一个面向用户的工具,用于水平丰度计算和数据集比较.
主要成果:
- PaxDb v6.0显著扩展了所有生命王国的覆盖范围,几乎翻了一番之前的数据集集成.
- 一个新的自动化管道确保了MS原始数据的一致再处理,提高了数据质量和可靠性.
- 更新的数据库包括标准化元数据,正义信息,以及集成数据集的质量评分.
- 新的工具有助于直接比较用户数据与PaxDb参考蛋白质组.
结论:
- PaxDb v6.0 在创建标准化,高覆盖率的蛋白质丰度参考资源方面取得了重大进展.
- 自动化再处理管道和增强的数据集成克服了公共MS数据重复使用的关键限制.
- 这个更新的资源通过提高可复制性和实现跨研究数据集成,促进了新的生物见解.
相关概念视频
01:33Proteomics
9.3K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.3K
02:26Protein Networks
4.5K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
02:26Protein Networks
2.8K
2.8K
02:26Conservation of Protein Domains Over Different Proteins
14.0K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.0K
02:47Protein Families
16.6K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
16.6K