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Related Concept Videos

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...
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...
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-Resolution Mass Spectrometry (HRMS)01:15

High-Resolution Mass Spectrometry (HRMS)

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 example, the mass of helium...
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...
Mass Spectrometers01:16

Mass Spectrometers

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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  3. Librarian: An Open-access Web Application For High-resolution Mass Spectral Library Assembly.
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  3. Librarian: An Open-access Web Application For High-resolution Mass Spectral Library Assembly.

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

Librarian: An Open-Access Web Application for High-Resolution Mass Spectral Library Assembly.

Jacob Ahlberg Weidenfors1, Bénilde Bonnefille2,3, Stefano Papazian2,3

  • 1Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden.

Metabolites
|June 25, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

Librarian is a new web application that simplifies the creation and sharing of mass spectral (MS2) libraries. This tool helps researchers build standardized, metadata-rich spectral records for improved chemical annotation in mass spectrometry.

Keywords:
FAIRHRMSMS-DIALMassBankNTAexposomicsmass spectrometrymetabolomicsopen-sourcespectral database

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Area of Science:

  • Mass spectrometry
  • Computational chemistry
  • Data science

Background:

  • High-quality tandem mass spectral (MS2) libraries are crucial for accurate chemical annotation in small-molecule mass spectrometry.
  • Current challenges in standardizing and sharing MS2 data limit community participation and the growth of open-access repositories.
  • Development of computational tools is needed to facilitate the creation and dissemination of MS2 reference libraries.

Purpose of the Study:

  • To develop a user-friendly, scalable web application for assembling standardized, metadata-rich MS2 spectral records.
  • To lower technical barriers for researchers contributing to open-access spectral databases.
  • To promote broader community engagement in the development and sharing of high-resolution MS2 libraries.

Main Methods:

  • Developed Librarian, a free, open-access web application for rapid MS2 library assembly.
  • Integrated automated retrieval of chemical identifiers and metadata from PubChem.
  • Facilitated compound mixture design for high-resolution mass spectrometry (HRMS) acquisition and curated MS2 spectra assembly.
  • Ensured compatibility with public spectral databases and open-source pre-processing tools.

Main Results:

  • Librarian provides an intuitive workflow for creating repository-ready MS2 records.
  • Demonstrated Librarian's utility by generating and depositing over 1500 new MS2 records into MassBank.
  • Successfully applied the generated library in retrospective analysis of environmental datasets.

Conclusions:

  • Librarian effectively streamlines the generation of standardized, metadata-rich MS2 reference records.
  • The application addresses a significant bottleneck in spectral library development and sharing for the scientific community.
  • Librarian supports the expansion of open-access resources vital for metabolomics, exposomics, and environmental mass spectrometry research.