Mass Spectrometry Blog

FREE Master Class on Effective Use of Mass Spectral Databases

Mass spectral libraries are a powerful tool for the identification of organic compounds in complex mixtures by mass spectrometry. This masterclass will demonstrate the use of the NIST (National Institute of Standards and Technology) software suite for accessing Wiley, NIST, and even user-generated libraries. The software includes MS Search, MS Interpreter, and AMDIS plus ChemSketch for structural drawing. 

This free masterclass is useful to a wide variety of research and developments scientists involved in medical, environmental, industrial, forensic, and biological disciplines.

Initial sessions will primarily discuss electron ionization gas chromatography/mass spectrometry (EI GC/MS) data. However, many of the principles are applicable to tandem spectra obtained by liquid chromatography/mass spectrometry (LC/MS) which will be discussed in the latter part of the series.

Detailed PDF handouts that support the presented content can be downloaded at the end of each class.

Part I: Spectral Searches with NIST MS Search

The initial presentation will discuss the use of the NIST search software for the identification of compounds using EI spectra obtained by GC/MS utilizing commercial databases. It is critical that the user is familiar with the setup of the program in order to obtain proper search results in the desired presentation format. The libraries can be searched by spectrum, AS No., names, molecular weight, molecular formulae, etc.

Part II: Structure Searches with NIST MS Search

The second part of the masterclass will address the search of commercial and user-generated databases by similar and exact structure. This is a powerful tool for finding model compounds in support of user-proposed identifications. MS interpreter is an integral function within the NIST MS Search program for correlating observed mass spectral fragmentation patterns with structures for both EI and tandem spectra.

Part III: AMDIS for Processing EI Mass Spectral Data Files

The third part of the masterclass will show the basics of AMDIS (Mass Spectral Deconvolution and Identification System) for processing EI GC-MS files. The spectra obtained by either deconvolution or manual subtraction are then sent to the MS Search program for characterization. The importance of obtaining high quality data from a user's GC/MS file to yield useful results will be emphasized. Most vendors' data processing programs can be utilized to process and then send data to the MS Search program for processing. However, due to time limitations, only AMDIS will be discussed.

Part IV: Advanced NIST Hybrid Search of EI and Tandem Spectra

Part four discusses an exciting new search algorithm within the MS Search program. This approach greatly extends the scope of the libraries by employing a "nearest neighbour" concept that locates hits differing by various functional groups. A hybrid score ranks the results and merges the more traditional fragmentation match factors with ones determined from neutral losses. The results are presented in a very novel format which greatly enhances visual interpretation of the results.

Part V: Creating and Sharing User EI and Tandem Libraries

The NIST search includes an approach for creating and sharing EI and tandem user-generated libraries. The libraries can be updated and archived nightly and searched with commercial databases to yield summed results. The software is run on basic PC hardware and is driven by custom-written batch files using a PC scheduling program.



Presented by James Little, Mass Spectral Interpretation Services

James Little Master ClassJames has been a contract worker for the NIST since 2016 as well as a research fellow at Eastman Chemical Company in Kingsport, Tennessee, USA for over 40 years. Specialties include: Corporate mass spectral databases, GC-MS, LC-MS, chemical ionization, and sample derivatization. James also has extensive NMR experience, both quantitative and qualitative as well as drug analysis by LC-MS in plasma.


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