Mass Frontier Spectral Interpretation Software

More unknowns can be confidently identified with MSⁿ and substructure spectral matching, utilizing the full power of structure retrieval from online databases or user provided structures.

The many precursor and MSⁿ fragmentation spectra are logically organized into Spectral Trees for each compound within mzCloud. Each level of a spectral tree symbolizes an MSⁿ stage, where the top level starts at n=1, or the precursor spectra. Each level can contain numerous spectra, as data are acquired using various different experimental conditions to ensure a broad and representative coverage of subsequent fragments, increasing the likelihood of high-quality search results.

A schematic representation of a spectral tree from mzCloud. The MS spectra are acquired for a given compound in multiple polarities (ESI +/-), and for a range of adducts. Each precursor is exhaustively fragmented using different fragmentation techniques (CID, HCD) and at multiple collision energies to produce collections of fragmentation spectra at each fragmentation level (MS², MS³, MS⁴ etc.), generating a comprehensive spectral tree of information for each library entry.

The extensive data for each library entry is critical for accurate compound identifications, matching experimentally obtained data to that of the library contents, with fit confidence and data visualization provided in the Compound Discoverer and Mass Frontier data analysis software packages. Additional tools include mzLogic, which uses the extensive fragmentation information to confidently identify unknowns that cannot be identified based upon the spectral library compound entries alone.

Using the extensive fragmentation data contained within mzCloud or your own curated spectral libraries, Mass Frontier software has several different search types available to increase the probability of matching some or all your spectral data to rapidly provide you with greater insights into your datasets:

• MS² vs MS² identify search
• MSⁿ vs MSⁿ tree search
• Identity substructure search (MSⁿ vs MSⁿ)
• Subtree Search (MSⁿ vs MSⁿ)
• mzLogic

Used to identify compounds, the MS² vs MS² identify search compares MS² spectra from the query tree to MS² spectra from mzCloud or reference library being used; the precursor ion must also match in both spectra for a match to be made. The resulting Identity score is based upon the information overlap from both matched MS² spectra.

The MSⁿ vs MSⁿ tree search is like the MS² vs MS² identify search, but it will search any of the Query MSⁿ trees against mzCloud or the reference library. Any matched fragmentation spectra are highlighted with a red border, with more matching MSⁿ spectra giving rise to an increase in the resulting match score.

A key benefit of the MSⁿ vs MSⁿ tree search, is that it can help to distinguish between positional isomers with greater confidence than the MS² vs MS² identify search due to the increased potential for structurally diagnostic fragment ions to be present in the higher-order fragmentation spectra being searched.

When there are no exact matches available within the queried library, the identity substructure search (MSⁿ vs MSⁿ) still allows you to make use of any extensive substructural information. Compounds that belong to the same compound class, or share a common substructure, can be identified through matching any MSⁿ spectra between the Query tree and the spectral tree from the searched library.

Being similar to the identity substructure search, the subtree search (MSⁿ vs MSⁿ) again seeks to match substructures from the library based upon MSⁿ spectral matching; the main difference is the use of multiple spectra, resulting in a different match score calculation and potential confidence in any match assignment.

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An example of an included Metabolika biological pathway, which can be fully edited and added to.

Confident structural elucidation through the use of automated fragmentation annotation of MSⁿ spectral trees. Fragmentation pathways can also be predicted based upon submission of a structure, and makes full use of the HighChem Fragmentation Library™: this contains information from more than 52,000 fragmentation schemes, 217,000 individual reactions, 256,000 chemical structures and 216,000 decoded mechanisms from peer reviewed literature.

Fragment Ion Search, or FISh, provides fast screening of structurally similar compounds based on the fragmentation pattern of the parent compound acquired either by theoretical fragment prediction or experimental MSⁿ spectral ion trees. FISh makes it quick and easy to identify relevant information because the parent compound structure and its potential metabolites are used to filter out the majority of matrix-related background ions. FISh provides extensive lists of Phase l and Phase ll biotransformations as well as the ability to build customized lists.

In addition to filtering the structurally similar compounds, FISh can automatically localize the modification site and label and apply color-coding to fragments common to both the parent and filtered results. In the example above, exact matches to proposed metabolite fragments are highlighted in green. Transformation-shifted matches are highlighted in blue.

Automated fragment assignments are generated using the HighChem Fragmentation Library, as described in the "Understanding fragmentation pathways" section.

The new curator module automates spectral tree curation, fragment annotation and mass recalibration for your proprietary compounds to build a high quality curated local MSⁿ library.