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

Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

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...
Experimental Determination of Chemical Formula02:37

Experimental Determination of Chemical Formula

The elemental makeup of a compound defines its chemical identity, and chemical formulas are the most concise way of representing this elemental makeup. When a compound’s formula is unknown, measuring the mass of its constituent elements is often the first step in determining the formula experimentally.
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...
Mass Spectrum01:23

Mass Spectrum

A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
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...
Mass Spectrometry: Overview01:19

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...

You might also read

Related Articles

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

Sort by
Same author

Tyrosine-sulfated peptide-induced flavonol biosynthesis controls elongation and differentiation in Arabidopsis primary root.

The Plant cell·2026
Same author

Mapping the soil microbiome functions shaping wetland methane emissions.

mSystems·2026
Same author

Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules.

Nature communications·2026
Same author

Bioengineered algal lipids enriched in structured medium- and long-chain triacylglycerols, linoleate, and <i>sn</i>-2 palmitate for human milk fat substitutes.

bioRxiv : the preprint server for biology·2026
Same author

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.

bioRxiv : the preprint server for biology·2026
Same author

Transcriptional and metabolic stasis define desiccation-induced dormancy in the soil bacterium <i>Arthrobacter</i> sp. AZCC_0090 until water vapor initiates resuscitation.

mSystems·2026
Same journal

Strain-Level Food Surveillance of <i>Escherichia coli</i> Using a Specific-Nonspecific Hybrid Sensor Array Strategy.

Analytical chemistry·2026
Same journal

A Field-Portable Fe(IV)-Mediated Competitive Quenching Chemiluminescence Platform with a Synchronous Y-Shaped Flow-through Cell for Broad-Spectrum Quantification of Volatile Phenols.

Analytical chemistry·2026
Same journal

Single-Molecule Characterization of CRISPR-Cas12a for Amplification-Free Genetic Testing.

Analytical chemistry·2026
Same journal

Integrated Acoustofluidic Manipulation and Oscillation-Stabilized Magnetic Relaxation Biosensing for <i>Salmonella</i> Detection.

Analytical chemistry·2026
Same journal

A Self-Powered Sensing Platform Based on the Janus Heterostructure for Machine Learning-Assisted Dual-Mode Detection of 17β-Estradiol.

Analytical chemistry·2026
Same journal

Large Language Model-Generated Dietary Metabolite Biomarker Database Drives Deep Annotation of the Human Diet Metabolome.

Analytical chemistry·2026
See all related articles

Related Experiment Video

Updated: May 7, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

Richard Baran1, Trent R Northen

  • 1Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.

Analytical Chemistry
|September 17, 2013
PubMed
Summary
This summary is machine-generated.

Automated mass spectra interpretation and chemical formula calculation using RAMSI streamlines untargeted metabolomics. This robust method enhances metabolite identification by accurately assigning spectral features and calculating chemical formulas.

More Related Videos

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Published on: March 14, 2013

Related Experiment Videos

Last Updated: May 7, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)
07:34

Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS)

Published on: March 14, 2013

Area of Science:

  • Metabolomics
  • Mass Spectrometry
  • Natural Product Discovery

Background:

  • Untargeted metabolite profiling via liquid chromatography-mass spectrometry (LC-MS) is crucial for discovering novel metabolites and biomarkers.
  • Identifying unknown metabolites from complex spectral data is a significant challenge in metabolomics.
  • Manual interpretation of mass spectra for metabolite identification is time-consuming, lacks standardization, and is difficult to scale.

Purpose of the Study:

  • To develop an automated and robust procedure for mass spectra interpretation and chemical formula calculation in untargeted metabolomics.
  • To address the limitations of manual data inspection and improve the scalability and standardization of metabolite identification workflows.

Main Methods:

  • Developed RAMSI (Robust Automated Mass Spectra Interpretation), a computational tool utilizing mixed integer linear programming optimization.
  • Expressed chemical rules among related ions as linear constraints for integrated spectra interpretation and formula calculation.
  • Combined positive and negative polarity spectra and handled background ions without predefined neutral loss sets.

Main Results:

  • RAMSI effectively and accurately assigned spectral features and calculated chemical formulas for metabolites.
  • The automated procedure successfully identified protonated or deprotonated molecules ([M + H]+ or [M - H]-).
  • The method demonstrated robustness in the presence of background ions across 30 experimental mass spectra.

Conclusions:

  • RAMSI offers a standardized and automated solution for mass spectra interpretation and chemical formula calculation in untargeted metabolomics.
  • This approach significantly enhances the efficiency and reliability of metabolite identification workflows.
  • The tool facilitates the discovery of novel natural products and biomarkers by overcoming spectral interpretation bottlenecks.