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相关概念视频

Tandem Mass Spectrometry01:21

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...
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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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...
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Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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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...
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MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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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...
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Proteomics01:33

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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...
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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使用免费的计算工具导航基于质谱的蛋白质数据.

Shijie He1, Fangfei Zhang2

  • 1School of Life Sciences, Westlake University.

Journal of visualized experiments : JoVE
|September 8, 2025
PubMed
概括
此摘要是机器生成的。

本研究提供了初学者分析质谱蛋白质组学数据的指南,涵盖了数据依赖获取 (DDA) 和数据独立获取 (DIA) 方法. 它展示了使用FragPipe和DIA-NN等免费工具进行有效数据解释的工作流.

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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.
  • 计算生物学 计算生物学

背景情况:

  • 基于质谱 (MS) 的蛋白质组学,包括数据依赖获取 (DDA) 和数据独立获取 (DIA),在生物研究中至关重要.
  • 对于有效地搜索和分析这些复杂的蛋白质组数据集进行验证研究的证明有限.

研究的目的:

  • 为了说明搜索和分析DDA和DIA蛋白质组数据集的全面工作流程.
  • 为后处理蛋白质搜索结果提供必要的协议,包括生成火山图片和识别失调蛋白质.
  • 作为处理蛋白质组数据的研究人员的初学者指南.

主要方法:

  • 使用来自PRoteomics IDEntifications数据库 (PRIDE) 的一个DDA和一个DIA数据集.
  • 使用FragPipe (v22.0) 进行DDA数据分析,使用DIA-NN (2.1.0) 进行DIA数据分析.
  • 应用R代码用于下游后处理,包括统计分析和可视化.

主要成果:

  • 展示了一种清晰的,逐步的蛋白质组数据分析协议.
  • 成功生成了DDA和DIA数据集中的火山图表和失调蛋白质列表.
  • 验证了免费计算工具的实用性,以进行可靠的蛋白质原子数据解释.

结论:

  • 这项工作提供了搜索和分析蛋白质组数据的基础协议,赋予研究人员权力.
  • 展示的工作流程可以有效地处理和解释基于MS的蛋白质组学数据集.
  • 研究人员可以利用这些方法来加强使用蛋白质组数据的生物研究.