scholarly journals Ion Identity Molecular Networking in the GNPS Environment

2020 ◽  
Author(s):  
Robin Schmid ◽  
Daniel Petras ◽  
Louis-Félix Nothias ◽  
Mingxun Wang ◽  
Allegra T. Aron ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Network Connectivity ◽  
Molecular Networks ◽  
Tandem Mass ◽  
Molecular Networking ◽  
Tandem Mass Spectra ◽  
Fragmentation Behavior ◽  
Fragmentation Patterns ◽  
Spectral Libraries ◽  
Ion Species

AbstractMolecular networking connects tandem mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.

scholarly journals Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Robin Schmid ◽  
Daniel Petras ◽  
Louis-Félix Nothias ◽  
Mingxun Wang ◽  
Allegra T. Aron ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Network Connectivity ◽  
Molecular Networks ◽  
Molecular Networking ◽  
Fragmentation Behavior ◽  
New Feature ◽  
Fragmentation Patterns ◽  
Spectral Libraries ◽  
Ion Species

AbstractMolecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.

scholarly journals reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

2015 ◽  
Vol 26 (11) ◽  
pp. 1837-1847 ◽  
Author(s):  
David Shteynberg ◽  
Luis Mendoza ◽  
Michael R. Hoopmann ◽  
Zhi Sun ◽  
Frank Schmidt ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Tandem Mass ◽  
Tandem Mass Spectra ◽  
Ion Species
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