Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.3K
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...
2.3K
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

2.7K
An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
2.7K
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

1.6K
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...
1.6K
Mass Spectrometers01:16

Mass Spectrometers

8.3K
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:
8.3K
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

8.3K
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...
8.3K
High-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

2.4K
The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
2.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Integrating multi-omics data for next-generation cancer research and precision medicine.

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·2026
Same author

Proteomics of human duodenum in pre-diabetes and type 2 diabetes reveals potential novel therapeutic targets for aetiology and therapeutics.

Clinical proteomics·2026
Same author

Metabolic reprogramming regulates histone lactylation during zebrafish caudal fin regeneration.

iScience·2026
Same author

Integrative Proteomics of Extracellular Vesicles from hiPSC-Derived Cardiac Organoids Reveals Heart Tissue-like Molecular Representativity.

International journal of molecular sciences·2026
Same author

LAMP2A regulates endosomal protein composition and membrane identity in exosome biogenesis.

iScience·2026
Same author

Intraductal Carcinoma Predicts Poor Response to Neoadjuvant Therapy in High-risk Prostate Cancer: A Retrospective Analysis of a Prospective Trial.

European urology open science·2025
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jan 19, 2026

Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems
14:42

Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems

Published on: September 23, 2021

5.7K

LC-MS Spectra Processing.

Rune Matthiesen1

  • 1Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal. runem2009@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2019
PubMed
Summary
This summary is machine-generated.

Accurate mass spectrometry data analysis relies on precise peak extraction from raw data. This study discusses peak processing methods and software in R for improved LC-MS data quality and accurate m/z value determination.

Keywords:
DechargingDeisotopingNoise filteringPeak extraction

More Related Videos

A Strategy for Sensitive, Large Scale Quantitative Metabolomics
14:18

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Published on: May 27, 2014

21.6K
Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures
09:38

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Published on: January 7, 2019

9.1K

Related Experiment Videos

Last Updated: Jan 19, 2026

Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems
14:42

Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems

Published on: September 23, 2021

5.7K
A Strategy for Sensitive, Large Scale Quantitative Metabolomics
14:18

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Published on: May 27, 2014

21.6K
Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures
09:38

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

Published on: January 7, 2019

9.1K

Area of Science:

  • Analytical Chemistry
  • Biochemistry
  • Computational Biology

Background:

  • Peak extraction is critical for Liquid Chromatography-Mass Spectrometry (LC-MS) data analysis.
  • The accuracy of peak extraction significantly impacts downstream analyses like database searching and quantitation.
  • Overlapping peaks can compromise the integrity of measured m/z values, a key physical entity in mass spectrometry.

Purpose of the Study:

  • To discuss current peak processing methods in LC-MS data analysis.
  • To highlight unresolved or neglected issues in peak extraction algorithms.
  • To present software solutions, particularly R packages, for spectra processing and generating Mascot Generic Files (MGF).

Main Methods:

  • Review of existing peak extraction algorithms for LC-MS data.
  • Discussion of strategies to handle overlapping peaks and ensure accurate m/z value determination.
  • Exploration of R software packages for spectral data processing and MGF file generation.

Main Results:

  • Identified key challenges in peak processing, including handling complex spectral data and overlapping signals.
  • Highlighted the importance of robust algorithms for accurate m/z value extraction.
  • Showcased the utility of R-based software for LC-MS spectral processing and data conversion.

Conclusions:

  • Effective peak processing is fundamental for reliable LC-MS data analysis.
  • Addressing challenges in peak extraction improves the accuracy of subsequent analytical steps.
  • R software offers valuable tools for enhancing LC-MS data processing workflows and data sharing.