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Related Concept Videos

Chemical Ionization (CI) Mass Spectrometry01:21

Chemical Ionization (CI) Mass Spectrometry

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The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the...
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CCSfind: A tool for chemically informed LC-IM-MS database building.

Sangeeta Kumari1, Tim Causon2

  • 1Core Facility Bioinformatics, BOKU University, Vienna, Austria.

Journal of Mass Spectrometry : JMS
|May 13, 2024
PubMed
Summary
This summary is machine-generated.

A new tool, CCSfind, enables comprehensive databases from ion mobility-mass spectrometry (IM-MS) data. It captures full ion mobility spectra and adducts, improving small molecule analysis and database building.

Keywords:
SQLiteconformersdrift tube IM‐MSpeak pickingprotomerspython

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Area of Science:

  • Analytical Chemistry
  • Computational Chemistry
  • Spectrometry

Background:

  • Ion mobility-mass spectrometry (IM-MS) provides accurate mass and ion conformation/size data (mobility K, collision cross section CCS).
  • Current analytical databases do not fully capture IM-MS data, such as full mobility spectra (CCS distributions) or additional ion species (e.g., adducts).
  • This limits the comprehensive utilization of experimental IM-MS measurements for small molecules.

Purpose of the Study:

  • To introduce CCSfind, a novel computational tool for building comprehensive databases from experimental IM-MS measurements.
  • To enable the unified processing and storage of full ion mobility spectra and diverse ion species within a single data step.
  • To enhance the analytical utility of IM-MS data for small molecule characterization and database creation.

Main Methods:

  • CCSfind parses open-source mzML files to target predicted ion species based on input chemical formulae.
  • The tool handles both chromatographically separated isomers and IM-separated isomeric ions (protomers, conformers).
  • User-defined SQL output format allows for simple database entry creation, with efficient processing of large files (up to 1 GB in <2 min).

Main Results:

  • CCSfind successfully builds comprehensive databases from experimental IM-MS data, integrating full mobility spectra and various ion species.
  • The tool efficiently processes large datasets, with computational time scaling linearly with input file size or number of molecular formulae.
  • Results can be manually reviewed and annotated with experimental settings before database commitment, ensuring data integrity.

Conclusions:

  • CCSfind represents a significant advancement in leveraging IM-MS data for small molecule analysis by enabling comprehensive database construction.
  • The tool addresses the limitations of current databases by capturing the full richness of IM-MS experimental data.
  • CCSfind facilitates improved data management and retrieval for IM-MS studies, supporting more detailed molecular characterization.