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Related Concept Videos

Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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...
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Mass Analyzers: Overview01:13

Mass Analyzers: Overview

1.0K
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...
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Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

6.8K
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 electrospray 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...
6.8K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

1.5K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
1.5K
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

4.1K
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...
4.1K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

1.8K
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 low-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...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Mass Dynamics 1.0: A Streamlined, Web-Based Environment for Analyzing, Sharing, and Integrating Label-Free Data.

Joseph Bloom1, Aaron Triantafyllidis1, Anna Quaglieri1

  • 1Mass Dynamics, C/O Hub Southern Cross, Level 2, 696 Bourke Street, Melbourne, Victoria 3000, Australia.

Journal of Proteome Research
|October 14, 2021
PubMed
Summary

Mass Dynamics 1.0 (MD 1.0) offers a cloud-based platform for analyzing label-free quantification (LFQ) proteomics data. It reliably quantifies protein expression, enhances reproducibility, and facilitates collaboration for researchers.

Keywords:
MaxQuantautomated data analysisbenchmarkinglabel-free quantificationweb-based software tool

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Label-free quantification (LFQ) is crucial for determining relative protein abundance in shotgun proteomics.
  • Existing analytical pipelines and visualization tools often lack integrated data storage and collaboration features.

Purpose of the Study:

  • To introduce Mass Dynamics 1.0 (MD 1.0), a web-based, cloud-based analysis environment for LFQ proteomics data.
  • To provide a platform for automated processing, visualization, annotation, sharing, and publication of LFQ results.
  • To enhance reproducibility and standardization in proteomics data analysis.

Main Methods:

  • MD 1.0 analyzes LFQ data generated by software like MaxQuant.
  • It utilizes a cloud-based architecture for data storage and processing.
  • The platform automatically generates quality control reports and requires minimal parameter choices.

Main Results:

  • MD 1.0 provides reliable protein expression quantification results.
  • Performance was benchmarked against Perseus, showing comparable results over a wide dynamic range.
  • The platform supports data annotation and sharing functionalities.

Conclusions:

  • MD 1.0 is a robust and user-friendly platform for LFQ proteomics data analysis.
  • Its cloud-based architecture and collaborative features streamline research workflows.
  • The tool promotes reproducibility and standardization in the field of proteomics.