Posted by: tvasailor | May 23, 2012

In Silico MS Fragmentation Data

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Eastman employs four different”in silico” software programs for processing MS/MS (CID) and EI spectra in our identification efforts.  The results are definitely not as useful as searching or examining experimentally acquired CID spectra.  Nevertheless, the use of in silico software programs and their associated spectra can definitely assist in shortening the time it takes to manually interpret and prioritize substructural information for candidate species.  In addition ABSciex has some interesting in silico capabilities and a section of a recent review article discusses the topic.

The software programs we use are listed below.

1.  Use of NIST MS Interpreter for EI and MS/MS Spectra

We routinely use NIST MS Interpreter to understand EI and MS/MS (APCI, electrospray) spectra.  It is critical part of entering compounds into both our EI and MS/MS libraries.  It quickly allows us to determine if all the major fragments in our spectrum are consistent with the proposed structure.  In addition, it can also be used to correlate fragment ions in a model compound’s spectrum to its substructure in the NIST and Wiley EI and MS/MS libraries and our in-house libraries.


It is supplied free of charge with the NIST Version 2.0 Software.  I have included screenshots of the MS Interpreter and a poster presented by NIST:

ms_interpreter_screenshots (2 pages)


2.  MetFrag with SciFinder and ChemSpider

MetFrag looks very interesting.  It allows me to use an automated connection to ChemSpider and a manual connection to SciFinder to obtain candidate structures.  In silico CID spectra are generated for all the candidate structures which are then compared to my acquired accurate mass CID spectrum.  The best results appear to be obtained in my examples by sorting by the “# of Explained Peaks” instead of “Score” in many cases.

I have shown the results for the approach with both ChemSpider and SciFinder for trazodone:


Their web links are:



If you want to try the trazodone example, the following link contains the mass spec data and the SDF file needed for the MetFrag query:


3.  Identifying “Known Unknowns” Using ChemSpider and Automated MS/MS Structure Correlation

A poster session was given at the 2012 ASMS conference in Vancouver.  The work was done as a collaborative effort between Agilent, ChemSpider (RSC), and Eastman Chemical Company.  The approach is described below with a link to the poster session in PDF format:

  • Accurate mass data acquired by LC/MS in data-dependent MS/MS mode
  • Agilent MassHunter Qualitative Analysis software used to find compounds and generate molecular formulas using monoisotopic mass, isotope abundance, and isotope spacing, as well as look for matching formulas for each fragment ion and its neutral loss from the precursor
  • Prototype Agilent MassHunter Molecular Structure Correlator software uses ChemSpider interface to obtain candidate structures for a target molecular formula and associated number of references for candidate structures
  • Calculation of correlation scores to explain MS/MS fragmentation pattern for each candidate structure using a “systematic bond-breaking” approach
  • Results sorted by number of references and/or correlation score to evaluate structure candidates for identification of components


3.   MathSpec

MathSpec, Inc. is a privately held company based in the Chicago area. The founder, Dr. Daniel L. Sweeney, believes that mass spectral fragmentation data can best be interpreted by viewing small molecules as mathematical partitions of the molecular weight. Dan has been doing LC-MS and interpreting MS/MS data for over twenty years.

It seems to work well and he is also modifying to find similar compounds.  He added the capability to sort by number of associated synonyms which is similar to the concept of sorting by the number of references in other programs.


Also see his You Tube videos describing his new software including add-ins in Excel.  Just search with Google for “MathSpec You Tube.”

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