在非目标代谢学中,对并联质谱进行可扩展的增量聚类
Xianghu Wang1, Deepa D Archarya2, Christopher J Brown3
1Department of Computer Science and Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States.
Journal of proteome research
|February 19, 2026
概括
我们开发了一个可扩展的集群框架,用于并联质谱 (MS/MS) 代谢学数据. 这种方法有效地处理数百万个光谱,克服大规模研究的计算瓶.
科学领域:
- 分析化学 分析化学
- 计算生物学 计算生物学
- 代谢学 代谢学 代谢学
背景情况:
- 双重质谱 (MS/MS) 对于非目标代谢学至关重要,产生大量的光谱数据.
- 当前的集群方法面临着计算和内存的限制,阻碍了对大规模和不断增长的MS/MS数据集的分析.
- 这些局限性影响长期研究和公共数据库,需要可扩展的解决方案.
研究的目的:
- 为处理大规模的MS/MS代谢学数据提供一种新的,可扩展的集群框架.
- 解决与现有的集群算法相关的计算和内存瓶.
- 在长期研究和公共存储库中对不断增长的MS/MS数据集进行有效分析.
主要方法:
- 开发了一个用于MS/MS代谢学数据的增量聚类框架.
- 实施了一种新的频谱聚合策略,通过在数据批次中传播局部密度结构来维持聚类性能.
- 在蛋白质组学数据集上使用基于数据库搜索的指标和在代谢组学数据集上使用MS1-保留时间 (MS-RT) 方法评估性能.
主要成果:
- 增量集群方法在集群纯度和完整性方面实现了与最先进的方法相提并论的性能.
- 通过在10,000个CPU小时内成功将3.68亿个光谱集成到数百万个集群中,证明了可扩展性.
- 由于过度的内存或时间要求,传统方法无法完成此任务,突出显示了可扩展性的优势.
结论:
- 拟议的可扩展的集群框架为分析大规模,不断增长的MS/MS代谢学数据集提供了实际解决方案.
- 该方法适合集成到GNPS2等公共代谢学平台中,从而提高数据可访问性和分析能力.
- 这一进步克服了当前代谢学数据处理的关键局限性,使得下游分析更全面.
相关概念视频
Tandem Mass Spectrometry
2.6K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
2.6K
Peptide Identification Using Tandem Mass Spectrometry
8.7K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
8.7K
Mass Spectrometry: Complex Analysis
1.9K
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
1.9K
High-Resolution Mass Spectrometry (HRMS)
2.7K
The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
2.7K
MALDI-TOF Mass Spectrometry
7.1K
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
7.1K
Mass Spectrometry: Overview
9.1K
Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...
9.1K


