在MSFragger中进行新的详细的质量偏移搜索,以改进复杂PTM的解释
Carolina Rojas Ramírez1, Fengchao Yu1, Daniel A Polasky1
1Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States.
Journal of proteome research
|January 13, 2026
概括
在MSFragger中进行详细的质量偏移 (DMO) 搜索,可以同时识别多种蛋白质修饰. 与开放式或标准质量偏移搜索相比,这种方法可以提高结果的解释和量化准确性.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 计算生物学 计算生物学
- 生物化学 生化学
背景情况:
- 传统的蛋白质组学数据库搜索在识别多个同时发生的蛋白质修饰时面临挑战.
- 开放式或宽容错误的搜索可以改善检测,但会使下游数据的解释和量化变得复杂.
- 现有的质量偏移搜索提供了一个中间道路,但缺乏氨基酸位点特异性.
研究的目的:
- 在MSFragger引擎中引入一种新的"详细"质量偏移 (DMO) 搜索策略.
- 增强多种蛋白质修饰的同时识别和特定位置定位.
- 为了提高复杂的蛋白质组数据集的解释性和量化.
主要方法:
- 在MSFragger软件中执行DMO搜索.
- 开发单个质量偏移的特定地点限制和碎片化规则.
- 将DMO搜索应用于复杂的修改集,包括翻译后修改,FPOP衍生修改和氨基酸替代.
主要成果:
- 在DMO搜索中,在不同数据集中同时成功识别了数百个修改.
- DMO搜索显著减少了网站定位的模糊性,特别是在重叠质量的修改方面.
- 随着搜索复杂度的增加,结果的可解释性和可扩展性得到了改善.
结论:
- 对于蛋白质组分析的现有质量偏移方法来说,DMO搜索是一个显著的进步.
- 这种方法提高了复杂的蛋白质组数据的准确性和易于解释的多重修改.
- DMO搜索为大规模蛋白质组研究提供了强大的工具,涉及广泛的修饰分析.
更多相关视频
07:01Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
817
06:47Expanding the Comprehension of the Tumor Microenvironment using Mass Spectrometry Imaging of Formalin-Fixed and Paraffin-Embedded Tissue Samples
Published on: June 29, 2022
2.5K
相关概念视频
Tandem Mass Spectrometry
2.3K
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...
2.3K
Mass Analyzers: Overview
1.6K
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
1.6K
MALDI-TOF Mass Spectrometry
6.5K
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...
6.5K
Mass Spectrometry: Molecular Fragmentation Overview
5.4K
The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
5.4K
Mass Spectrum: Interpretation
2.7K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
2.7K
Peptide Identification Using Tandem Mass Spectrometry
8.1K
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...
8.1K
