LC/MS Unknown Identifications Using MSMS Libraries Part III: More Detailed Discussion of MSMS Hybrid Search

Fr, 5.3.2021
| Original article from: Mass Spec Interpretation Services/James Little
A series of videos exploring the use of NIST Search Software for the identification of unknowns using tandem (MS/MS) spectra.
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Mass Spec Interpretation Services/James Little: More Detailed Discussion of MSMS Hybrid Search

MS/MS (Tandem) spectra can be used to identify unknowns employing library searches. This is accomplished in much the same approach as that employed for EI GC-MS with the NIST search software. The much improved NIST Search Version 2.4 is included with the 2020 library release.

I will attempt to introduce the user to the use of the NIST Version 2.4 search software employing NIST, Wiley, “crowd-sourced (MoNA)”, and user libraries for the identification of unknowns.

NIST has an ambitious program to extend their already comprehensive, high-quality MS/MS databases.

See the following link: NIST Pipeline for Extending MS/MS Libraries

This involves a very comprehensive process for selecting pertinent compounds for purchase and subsequent analyses. The problem with variability of the spectra is reduced by analyzing the samples on a variety of instruments at a variety of energy levels (20 steps). In addition, many different precursor ions and fragment ions are characterized (MSⁿ). This has already led to a very large high quality library of accurate mass MS/MS spectra in the 2020 release version (31K compounds/1.3 M spectra) and the effort is ongoing.

The Part III will cover:

Detailed Handouts including tables of content are available in the LabRulezLCMS library.

  • Introduction to Presenter, James Little
  • Table of Contents
  • Series of Talks: LCMS Unknown Identifications Using MSMS Libraries
  • Help Files for NIST Search
  • NIST Software in General is “Windows Compliant”
  • Presentation Topics
  • Program Description and My Personal Experience
  • Comparison to Standard versus Neutral Loss Spectrum
  • Hybrid Search Results for Example
  • Using DotProduct Instead of Score for Viewing Results
  • DeltaMass Table
  • Simple Examples Using Structures to Show DeltaMass
  • Viewing Peak Matching Results by Sorting in Hybrid Search Results
  • Merging Hybrid with Peak Matching Results
  • Detailed Explanation of Hybrid Head to Tail Display
  • Alternate Neutral Loss Comparison in Head to Tail Format
  • Other Things to Consider with Hybrid Search for Unknown Identification
  • Setting Up CriticalDefault Parameters for MS/MS Hybrid Search
  • Live Searching Demonstration YouTube Video
  • Acknowledgements

Future parts will focus on:

  • Part IV: Importing MSMS Spectra
  • Part V: NIST Structure Searches
  • Part VI: MS Interpreter Correlation of Substructure to MSMS Ions
  • Part VII: Using and Creating Other MSMS Libraries
  • Part VIII: Identification of Unknowns with “Spectraless” Libraries
James Little/Mass Spec Interpretation Services
 

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