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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...
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...
High-Performance Liquid Chromatography: Instrumentation00:57

High-Performance Liquid Chromatography: Instrumentation

High-performance liquid chromatography, or HPLC, is an analytical technique that separates liquid samples under high pressures. An HPLC instrument consists of glass bottles for storing solvents called mobile phase reservoirs. HPLC-grade solvents are used to maintain high purity, and the dissolved gases are removed using a degasser, such as a vacuum pumping system or sparging with helium. The solvents are then pumped into the analytical column using a screw-driven syringe or reciprocating pumps.
High-Performance Liquid Chromatography: Introduction01:11

High-Performance Liquid Chromatography: Introduction

High-performance liquid chromatography(HPLC), formerly referred to as High-pressure liquid chromatography, is a powerful technique used to separate, identify, and quantify components in complex mixtures. The term "high pressure" refers to using high pressure to push the liquid mobile phase through the tightly packed columns.
In HPLC, two phases play a critical role in the separation process:
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...
Matrix-Assisted Laser Desorption Ionization (MALDI)01:08

Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI is an ionization technique, widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix...

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Related Experiment Video

Updated: Jul 14, 2026

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)
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VIPER: an advanced software package to support high-throughput LC-MS peptide identification.

Matthew E Monroe1, Nikola Tolić, Navdeep Jaitly

  • 1Pacific Northwest National Laboratory, Richland, WA 99354, USA.

Bioinformatics (Oxford, England)
|June 5, 2007
PubMed
Summary

The VIPER software package enhances large-scale proteomic experiments using the accurate mass and time (AMT) tag approach. It automates feature discovery, alignment, and quantification of peptides for complex biological data analysis.

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Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT)
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Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
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Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

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Area of Science:

  • Proteomics
  • Computational Biology
  • Biotechnology

Background:

  • Large-scale proteomic experiments generate vast amounts of complex data.
  • Accurate Mass and Time (AMT) tag approach enables robust analysis across multiple datasets and instrument types.
  • Software tools are crucial for processing and interpreting this data.

Purpose of the Study:

  • To introduce the VIPER software package as a key component for analyzing large-scale proteomic data.
  • To describe the automated algorithms within VIPER for LC-MS feature processing.
  • To highlight VIPER's capability in identifying and quantifying isotopically labeled peptides.

Main Methods:

  • Utilizes the Accurate Mass and Time (AMT) tag approach for data integration.
  • Employs automated algorithms for Liquid Chromatography-Mass Spectrometry (LC-MS) feature discovery.
  • Implements peptide matching against a database of identified peptides from LC-MS/MS analyses.
  • Facilitates identification and quantification of isotopically labeled peptide pairs.

Main Results:

  • VIPER successfully integrates information from multiple datasets and instrument types.
  • Automated algorithms enable efficient discovery and alignment of LC-MS features.
  • Accurate identification and quantification of peptides are achieved through database matching.
  • The software supports the analysis of complex, large-scale proteomic experiments.

Conclusions:

  • The VIPER software package is a vital tool for the data processing pipeline in large-scale proteomic studies.
  • VIPER leverages the AMT tag approach for comprehensive data analysis.
  • The software provides automated solutions for peptide identification and quantification, advancing proteomic research.