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Related Concept Videos

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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...
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 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...
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...

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

Published on: August 19, 2025

Annotator: postprocessing software for generating function-based signatures from quantitative mass spectrometry.

Juliesta E Sylvester1, Tyler S Bray, Stephen J Kron

  • 1Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States.

Journal of Proteome Research
|January 10, 2012
PubMed
Summary
This summary is machine-generated.

Annotator software aids researchers in analyzing mass spectrometry data, identifying significant protein changes and functional categories for a clearer understanding of cell behavior. This tool provides quantitative, data-driven insights for reproducible results.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Systems Biology

Background:

  • Mass spectrometry generates large datasets of protein abundance changes.
  • Analyzing these complex datasets for biological significance is challenging.
  • Current methods often lack quantitative relationships and hinder reproducibility.

Purpose of the Study:

  • To develop a novel application, Annotator, for postprocessing mass spectrometry data.
  • To provide a standardized and quantitative method for analyzing protein abundance changes.
  • To enable systems-level interpretation of proteomic data using functional categories.

Main Methods:

  • Filtering validated mass spectrometry data.
  • Applying standardized heuristic and statistical tests for significance.
  • Incorporating UniProt and Gene Ontology keywords as statistical units of analysis.

Main Results:

  • Annotator provides quantitative information on abundance changes for entire functional categories.
  • The application facilitates "bottom-up" annotations based on experimental data.
  • It offers a consistent method for interpreting cellular behavior changes.

Conclusions:

  • Annotator addresses the challenge of data interpretation in proteomics.
  • It enables reproducible and data-driven conclusions about cellular behavior.
  • The tool supports the dynamic nature of functional annotations in ongoing proteomic research.