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Related Concept Videos

Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

4.1K
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...
4.1K
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

8.2K
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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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...
2.1K
Mass Spectrum01:23

Mass Spectrum

5.3K
A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
5.3K
Mass Spectrometry: Isotope Effect01:13

Mass Spectrometry: Isotope Effect

4.3K
Most elements exist in nature as a mixture of isotopes. The isotopes differ in weight due to their respective number of neutrons. The molecular weight of a molecule is different depending on the specific isotope of its elements involved. As a result, the mass spectrum of the molecule exhibits peaks from the same fragment at multiple positions. The positions of these mass signals depend on the mass differences between isotopes. Furthermore, the intensity of these signals is dependent on the...
4.3K
Mass Spectrometers01:16

Mass Spectrometers

9.6K
This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
9.6K

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Updated: Apr 28, 2026

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry
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Employing ProteoWizard to Convert Raw Mass Spectrometry Data.

Jerry D Holman1, David L Tabb1, Parag Mallick2

  • 1Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.

Current Protocols in Bioinformatics
|June 19, 2014
PubMed
Summary

This protocol details using ProteoWizard software to convert raw mass spectrometry data from proprietary binary files into open formats. This conversion is essential for downstream analysis using bioinformatics tools and database search engines.

Keywords:
LC-MS/MSdatabase searchmzMLproteomicsraw files

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Area of Science:

  • Proteomics
  • Mass Spectrometry Data Analysis

Background:

  • Raw data from liquid chromatography-tandem mass spectrometry (LC-MS/MS) are typically stored in vendor-specific binary formats.
  • Interoperability between different software tools is crucial for efficient data analysis in biological research.

Purpose of the Study:

  • To provide a detailed protocol for converting raw LC-MS/MS data files into open-format files.
  • To guide researchers in utilizing ProteoWizard software for data conversion, considering various format features and vendor particularities.

Main Methods:

  • Utilizing the ProteoWizard software suite for data conversion.
  • Addressing specific considerations such as file formats, coding options, and vendor-specific data structures.

Main Results:

  • Successful conversion of proprietary binary mass spectrometry data to open formats.
  • Preparation of data for compatibility with common bioinformatics analysis software and database search engines.

Conclusions:

  • ProteoWizard offers a robust solution for converting LC-MS/MS data, enhancing data accessibility.
  • Standardizing data formats through conversion facilitates broader application of bioinformatics tools in proteomics research.