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Related Concept Videos

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...
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...
Proteomics01:33

Proteomics

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.
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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.
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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...
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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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A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
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A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

Published on: March 13, 2014

Multivariate approach for protein identification based on mass spectrometric data.

Jung Bok Lee1, Jae Won Lee

  • 11Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43 gil, Songpa-Gu, Seoul, South Korea.

Statistical Methods in Medical Research
|January 21, 2012
PubMed
Summary

This study introduces a new statistical model for protein mass spectrometry, improving protein identification accuracy. The method enhances the detection of medium and small proteins in large datasets.

Keywords:
generalized linear mixed modelmass spectrometryprotein identificationtwo-part model

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Last Updated: May 25, 2026

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry
08:04

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Protein mass spectrometry is crucial for protein identification.
  • Current database searching algorithms rely on heuristic or restrictive statistical approaches.
  • There is a need for more accurate and robust statistical methods in protein identification.

Purpose of the Study:

  • To develop an improved statistical model for protein mass spectrometry scoring.
  • To enhance the accuracy of protein identification, especially for medium and small proteins.
  • To provide a computationally feasible method for analyzing large datasets.

Main Methods:

  • Developed a statistical model using a generalized linear mixed model.
  • Employed penalized generalized weighted least squares for computation.
  • Incorporated match dependencies into a novel statistical scoring function using the beta-binomial distribution.

Main Results:

  • Achieved improved protein searching performance compared to existing methods.
  • Demonstrated feasible computation procedures for very large datasets.
  • Significantly increased accuracy in identifying medium and small proteins.

Conclusions:

  • The proposed statistical modeling offers a more accurate and feasible approach to protein identification via mass spectrometry.
  • This method addresses limitations of current algorithms, particularly for challenging protein targets.
  • The findings have implications for advancing proteomic data analysis and discovery.