Interchanging Structures Between KnowItAll and NIST Search and Basics on Using MS Interpreter

Significance of the Topic

Transferring chemical structures seamlessly between spectral databases like NIST Search and graphical editors such as KnowItAll ChemWindow is essential to accelerate mass spectrometry interpretation workflows and ensure consistency in QA/QC and research environments.

Objectives and Overview

This guide provides a comprehensive framework for interchanging molecular structures between NIST Search and KnowItAll ChemWindow, outlines three distinct transfer methods, and demonstrates how to integrate structures with the NIST MS Interpreter for detailed electron ionization fragmentation analysis.

Methodology

The workflow comprises:

1. Clipboard Exchange
   
   • Copy the molecular structure from a highlighted entry in NIST Search using “Copy Structure to Clipboard.”
   • Open a new Structure Document in ChemWindow and use “Paste Special” selecting MOL text.
2. File Association
   
   • Configure Windows Default Apps to associate the *.mol file extension with the KnowItAll ChemWindow executable.
3. Autoimp.str Utility
   
   • Create or edit the autoimp.str file in the NIST20/MSSEARCH folder to add KnowItAll as a context-menu option.
4. Reverse Transfer
   
   • Copy structures in ChemWindow using the standard Copy command (avoid “Copy As”).
   • In NIST Search, use “Insert Clipboard Structure” to import the drawing into the search list.

Used Instrumentation

This workflow employs:

• NIST Mass Spectrometry Search software (NIST20/MSSEARCH).
• KnowItAll ChemWindow structure editor.
• NIST MS Interpreter module for fragmentation elucidation.
• Microsoft Windows OS file association features.

Main Findings and Discussion

All three transfer methods are user-friendly: clipboard and file-association approaches require minimal setup, while the autoimp.str method offers permanent menu integration at the expense of manual script editing. Reverse transfers work reliably but may misrepresent aromatic rings drawn with circle notation; alternating double bonds are recommended. Integration with MS Interpreter allows mapping of observed ions to substructures, highlighting explained fragments in color and flagging unexplained peaks for deeper investigation.

Benefits and Practical Applications

The described interoperability eliminates manual redrawing of structures, reduces transcription errors, and enables simultaneous spectrum-structure visualization. These improvements boost productivity in industrial QA/QC, academic research labs, and routine spectral library maintenance.

Future Trends and Potential Applications

Emerging developments may include:

• API-based automated structure transfer between cloud-hosted spectral repositories and desktop tools.
• AI-driven fragmentation prediction models directly linked to spectral databases.
• Seamless integration of structure exchange into laboratory information management systems (LIMS) and electronic laboratory notebooks.

Conclusion

This guide demonstrates efficient strategies for exchanging molecular structures between NIST Search and KnowItAll ChemWindow, and for leveraging the MS Interpreter to gain fragmentation insights. Adopting these methods streamlines mass spectrometry workflows and enhances reliability of structural interpretation.

References

• Little J. Little Mass Spec and Sailing. Available at littlemsandsailing.wordpress.com.
• NIST Mass Spectrometry Search Manual, Version 2020.