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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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...
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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...
Mass Spectrometers01:16

Mass Spectrometers

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:
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

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...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

mzServer: web-based programmatic access for mass spectrometry data analysis.

Manor Askenazi1, James T Webber, Jarrod A Marto

  • 1Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School,Boston, MA 02115, USA.

Molecular & Cellular Proteomics : MCP
|January 27, 2011
PubMed
Summary
This summary is machine-generated.

Large-scale proteomics data requires new sharing methods. A web server (mzServer) provides programmatic access to raw mass spectrometry data, improving accessibility and re-analysis for biomedical research.

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Area of Science:

  • Biomedical research
  • Proteomics
  • Data science

Background:

  • Proteomics data generation is increasing exponentially.
  • Current data sharing practices are insufficient for large datasets.
  • Discovery-mode MS/MS analyses lead to incomplete data reduction and future re-analysis needs.

Purpose of the Study:

  • To propose a new paradigm for proteomics data sharing.
  • To address the limitations of current data distribution methods.
  • To facilitate programmatic access to raw mass spectrometry data.

Main Methods:

  • Development of a web-based server (mzServer).
  • Implementation of a common Application Programming Interface (API) called mzAPI.
  • Utilizing RESTful uniform resource locators (URLs) for data access.

Main Results:

  • mzServer provides remote data access and analysis capabilities.
  • The system enables programmatic access to raw data at the site of acquisition.
  • A prototype demonstrates a model for lab-based and community-wide data access.

Conclusions:

  • Programmatic access to raw proteomics data is essential for future research.
  • mzServer and mzAPI offer a scalable solution for data sharing.
  • This approach supports efficient data re-analysis and discovery in biomedical research.