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Related Concept Videos

Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

7.8K
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 electrospray 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...
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MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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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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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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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Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
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Mass Spectrometers01:16

Mass Spectrometers

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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:
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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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Related Experiment Video

Updated: Dec 6, 2025

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
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IP4M: an integrated platform for mass spectrometry-based metabolomics data mining.

Dandan Liang1, Quan Liu2, Kejun Zhou2

  • 1Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.

BMC Bioinformatics
|October 8, 2020
PubMed
Summary

A new bioinformatics tool, Integrated mass spectrometry-based untargeted metabolomics data mining (IP4M), offers comprehensive features for metabolomics data analysis. It supports both basic and advanced users with simplified workflows and customizable options for enhanced data mining.

Keywords:
Data analysisMetabolomicsSoftwareWorkflow

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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
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Area of Science:

  • Bioinformatics
  • Metabolomics
  • Computational Biology

Background:

  • Metabolomics data analysis necessitates bioinformatics tools.
  • Existing integrated platforms are widely used, but demand for alternative solutions persists for diverse user expertise.

Purpose of the Study:

  • To develop and introduce a novel, multi-functional software platform for untargeted metabolomics data mining.
  • To provide a comprehensive solution catering to both novice and expert users in computational metabolomics.

Main Methods:

  • Development of Integrated mass spectrometry-based untargeted metabolomics data mining (IP4M) software.
  • IP4M incorporates 62 functions across 8 modules, covering the entire data mining pipeline from preprocessing to pathway analysis.
  • Includes a KEGG-derived database, GRaMM method for metabolome-microbiome correlation, and simplified workflows.

Main Results:

  • IP4M software was successfully designed and developed, offering extensive functionalities for metabolomics data mining.
  • The software includes modules for data preprocessing, statistical analysis, biomarker detection, correlation analysis, and pathway enrichment.
  • Performance evaluation demonstrated IP4M's capabilities using diverse datasets (standards mixture, serum samples) from GC-MS and LC-MS.

Conclusions:

  • IP4M is a powerful, modular, customizable, and user-friendly software for metabolomics data processing and analysis.
  • The platform is suitable for a wide range of users, from beginners to experts.
  • Free versions are available for Windows, macOS, and Linux systems.