HighChem, Ltd. - Spectra Classifier

Spectra Classifier

Introducing Spectra Classifier

Mass Frontier can be used for the classification of spectra according to physical or chemical properties (point of origin, toxicity, aromaticity etc.). For spectra that cannot be found in a library, classification can involve identification of substructure types or compound classes (structure elucidation) in order to establish and confirm structural proposals. Classification can also be useful in cases when only structurally related compounds need to be retrieved from a complex chromatogram (metabolite research).

Open Spectra Classifier

The Spectra Classifier window is the gateway to PCA, SOM and Fuzzy Clustering. Any spectra that you wish to classify must first be sent or pasted to the Spectra Classifier window. A spectrum or spectra are automatically assigned to a group. Mass Frontier automatically gives a name to a new group, which can be easily renamed. The program also assigns a graphic representation to each group that is prepared for classification. Up to 255 groups of spectra can be added to Spectra Classifier and each group can consist of an unlimited number of spectra. Conversely, it is also possible for a group to only contain a single spectrum. The points are given symbol types and colors according to settings in Classification Layout. These settings only show group membership and have no influence on the results of the analysis

Spectra Classifier Window

There are two panes in the upper half of the Spectra Classifier window. The left one is a container of groups of spectra that have been sent from a Database Manager window. You can fill this pane successively with the spectra you have chosen for classification. Each group of spectra is visually represented as a single line in the left or right pane. The right pane contains the groups of spectra that will actually be classified, if you click the Classify Now button. You can move a group from one pane to another by clicking the Add and Remove button. The two-pane set-up allows you to have spectra available in the left pane, ready for inclusion in future classification runs.

Classifying Mass Spectra

A simple example should help clarify how the classification of mass spectra can be carried out. Suppose we wanted to classify the derivatives of nicotine and caffeine. We have an EI

spectrum of an unknown compound that we suspect is either a metabolite of nicotine or caffeine, and we need to find out which of these two compound classes it belongs to. To complete this task we need to retrieve sufficient amount of spectra for each group (e.g. nicotines and caffeines) which will then be submitted to a principal component analysis, to form clusters of each group. We can do this by performing a substructure search, where the search query will be the structure of nicotine and caffeine. If sufficient amount of spectra for each group are found (more than 10 spectra) you should select these records and add them, separately for each group, to the Spectra Classifier. Then you can assign an appropriate name to each group using the Selected Group of Spectra edit box. Feel free to use the copy (Ctrl C) and paste (Ctrl V) commands. Then, select a line in the left pane of Spectra Classifier and click on the Add button. Repeat this for the next group.

Maintaining Groups of Spectra

Mass Frontier allows the saving and opening of references to records with the extension *.ref , present in the Database Manager spreadsheet. This feature is especially useful for maintaining groups of spectra that are sent from Database Manager to the Spectra Classifier window. If you have retrieved spectra for classification, it is useful to save these records as references, rather then save the spectra as ASCII files (JCAMP or MSP). In contrast to JCAMP or MSP files, a reference file stores the locations, where all the relevant information about each spectrum is saved (spectrum, structure, experimental conditions etc.). In addition reference files are easy to manipulate, you can add or remove one or more records to them. Deconvoluted spectra from Chromatogram Processor cannot be saved as references.

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