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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...

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Related Experiment Video

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Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry
06:09

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Enhanced peptide quantification using spectral count clustering and cluster abundance.

Seungmook Lee1, Min-Seok Kwon, Hyoung-Joo Lee

  • 1Department of Statistics, Seoul National University, Korea.

BMC Bioinformatics
|November 1, 2011
PubMed
Summary
This summary is machine-generated.

A new method, Quantification method based on Finding the Identical Spectral set for a Homogenous peptide (Q-FISH), accurately identifies and quantifies peptides in mass spectrometry data. This approach enhances protein identification and discovers novel biomarkers for diseases like hepatocellular carcinoma.

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

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Last Updated: May 28, 2026

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry
06:09

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

  • Proteomics and Mass Spectrometry
  • Biomarker Discovery
  • Computational Biology

Background:

  • Label-free quantification methods like spectral counting and feature analysis rely on database searches and accurate retention time estimation, which have limitations.
  • Existing peptide identification methods often fail to provide optimal matches and cannot identify novel peptides not present in databases or spectral libraries.
  • There is a need for improved methods to overcome restrictive database searches and inaccurate retention time estimations in proteomics.

Purpose of the Study:

  • To introduce a novel method, Quantification method based on Finding the Identical Spectral set for a Homogenous peptide (Q-FISH), for peptide abundance estimation directly from MS/MS spectra.
  • To enhance protein identification accuracy by grouping replicated spectra of the same peptide targets.
  • To identify and quantify differentially expressed peptides in human hepatocellular carcinoma (HCC) and normal liver tissues.

Main Methods:

  • Q-FISH directly compares experimental spectra to estimate peptide abundance, identifying both known and novel proteins.
  • The method groups replicated spectra from identical peptide targets to improve identification accuracy.
  • Applied Q-FISH to Nano-LC-MS/MS data from HCC and normal liver tissues, followed by a beta-binomial test to identify differentially expressed peptides.

Main Results:

  • Q-FISH generated 14,747 clusters from 44,318 spectra, identifying peptides unique to HCC, normal tissue, or present in both.
  • A beta-binomial test identified 84 differentially expressed peptides between HCC and normal tissues.
  • Compared to SEQUEST, Q-FISH identified more known liver cancer biomarkers, including novel peptides associated with cancer.

Conclusions:

  • Q-FISH is a novel statistical method for accurate protein identification and simultaneous peptide quantification from mass spectrometry data.
  • Q-FISH analysis of HCC and liver tissues identified numerous protein biomarkers relevant to HCC.
  • Q-FISH offers a potentially more effective tool for peptide identification, quantification, and novel biomarker discovery compared to standard methods like SEQUEST.