HighChem Mass Frontier™ is a world leading software package for the management, evaluation and interpretation of mass spectral and chromatographic data. With its advanced algorithms, extensive libraries and superior graphical user interface, Mass Frontier is capable of solving analytical problems in a wide range of applications including metabolomics, forensics, environmental, natural products, impurities, and degradants research. (See complete description of Mass Frontier)
Structure Editor in Mass Frontier is specifically designed for mass spectrometry by supporting charged, protonated and deprotonated molecules; adducts, isotopes and substituents. Chemical structures drawn in Structure Editor can be used for spectra and chromatogram annotations, fragment prediction, user fragmentation libraries, sub-structure searches in more than 100,000 reaction mechanisms, PIF, FISh, or the consistency checking of a mass spectrum and chemical structure. In addition, when part of a structure is selected in Structure Editor, the molecular formula and mass of the selected atoms and the corresponding loss are displayed in the status bar.
A most outstanding feature in Mass Frontier is the automated generation of possible fragments at an expert level, including complete fragmentation and rearrangement mechanisms, starting from a user-supplied chemical structure. To predict the fragmentation reactions, Mass Frontier employs an expert system that automatically applies a suitable decomposition mechanism for any small molecule by using general fragmentation rules or Fragmentation Library™, or both. The knowledge base consists of 24 ionization, fragmentation and rearrangement rules along with more than 100,000 published fragmentation mechanisms.
A unique capability of Mass Frontier is its copyrighted Fragmentation Library™, which contains curated fragmentation mechanisms for small molecules. These mechanisms have been collated from available peer reviewed mass spectrometry literature. Each mechanism, along with the chemical structures, has been manually and automatically verified and saved in the library along with complementary information such as the title, authors and source of the information. Fragmentation Library contains 30,936 fragmentation schemes that contain more than 100,000 individual reaction mechanisms.
Back in 2004, HighChem introduced a new tandem mass spectra concept, coined Spectral Trees™, where multi-stage MSn spectra are organized as nodes in a tree structure. A Spectral Tree is a logically structured container of product ion spectra in which tree depth represents the MS stage, a node contains spectra with a common precursor ion, and node items hold spectra acquired in various experimental conditions such as different collision energies, isolation widths, zoom spectra, source CID spectra, filtered spectra, or any other spectra that enhance reproducibility in compound identification. Mass Frontier’s Spectral Trees can contain nodes with data-reduced chromatograms that can be assigned to every node, which allows for the storage of product ion chromatograms for a particular precursor m/z value. Spectral Trees are supported throughout the program; they can be stored in user libraries, extracted from chromatograms or used for the identification of unknowns using PIF.
Spectral Trees™ Library (MSn spectra) contains more than 13,000 high quality ion trap spectra of 1,251 positive and 524 negative ESI Spectral Trees of human and veterinary pharmaceuticals, endogenous metabolites, drugs of abuse, and doping agents. Each record contains a name, structure, and CAS number. In addition, 702 positive and 263 negative ESI spectral trees are annotated by fragment structures and associated with fragmentation mechanisms.
The automated system for detecting chromatographic components is capable of extracting the unique mass spectral features from closely coeluting components and the subsequent extraction of clean spectra or Spectral Trees (deconvolution) from GC/MS, LC/MS or LC/MSn runs. This system is designed for a broad selection of chromatographic experiments, GC/MS, LC/MS or LC/MSn, for clean and noisy signals, for simple or complex chromatograms, for low and high resolution, for full scan, data dependent or mode switching data files. The Components Detection and Spectra Deconvolution system involves the combined use of the following procedures: noise examination, signal filtering, smoothing, baseline definition and demarcation of chromatographic peaks, background scan determination, background subtraction, component candidate detection and model ion selection (m/z), correlation of model ion profiles and component confirmation or rejection, spikes elimination, calculation of exact component retention time, and spectra deconvolution using linear algebra.
Mass Frontier fully supports high resolution spectra. For correct spectra processing it is immensely important to use native high resolution data processing techniques, since they differ significantly from low resolution methods. Mass Frontier contains a wide range of advanced high resolution algorithms like spectra matching, noise filtering, peak alignment, component detection, formula generation and fragment prediction. The Spectral libraries do not only incorporate high resolution spectra, but also store indispensable pieces of information for every peak: mass resolution and accuracy.
Fragment Ion Search (FISh) is one of the most innovative and effective approaches available on the market for the detection and identification of metabolites. Using the FISh algorithm, all spectral and subsequent chromatographic peaks related to a metabolite are “fished out” and possible sub-structures for detected metabolites are displayed. The site of biotransformation can also be automatically localized using this approach. In contrast to traditional post-acquisition processing techniques, FISh eliminates the need for a prior structural prediction of biotransformations from the parent compound, and no subjective judgment in terms of parameter settings is required. Because of the outstanding sensitivity of this approach, even low abundant metabolites that were never previously reported can be detected.
Formula Generator Module calculates the possible elemental composition for any spectral peak or manually specified m/z value. Using this module, a complete spectrum annotation is possible. To eliminate unlikely theoretical molecular formulas, chemically intelligent features like the ring plus double bond equivalent can be chosen, and isotopic profiles of observed peaks and predicted formulas can be matched.
Powerful classification methods such as PCA, Neural Networks and Fuzzy Clustering complement the wealth of methods for interpreting mass spectral data in Mass Frontier. Classification is a powerful enhancement of the library search and fragmentation prediction methods. This provides possibilities for creating alternative strategies and enables effective data interpretation. From a user viewpoint, the important advantage of classification methods is the fact that there is no need for detailed knowledge of the complex spectra-structure relationship to achieve satisfactory results. The classification strategy in Mass Frontier is based on a user-friendly graphic presentation of the results, which can be easily viewed on the screen.
In all libraries, modules and algorithms, Mass Frontier supports chemical structures containing isotopes, specified or unspecified charge sites, aducts, substiruents, and protonated and deprotonated ions. For example, using substituents or isotopically labeled atoms, it is possible to specify the course of a rearrangement mechanism in a user fragmentation library. The fragments prediction feature understands all types of the above mentioned structures.
Mass Frontier includes a powerful database server that allows the management and administration of libraries over a computer network. Using the Server Manager application, it is possible to create, install, remove, delete, import, convert, back up, and restore spectral and fragmentation libraries on a local or network computer. A variety of server options and network topologies are supported.