Mass Frontier Spectral Interpretation Software

Solve your small molecule identification challenges

Confident small molecule unknown compound identification and structural elucidation can be labor intensive and time consuming. Simplify and streamline this challenge through the use of Thermo Scientific Mass Frontier software which utilizes the most high quality, fully curated experimental spectral and fragmentation libraries available to provide greater insights, understanding and confidence when turning your data into actionable knowledge.

Key benefits of Mass Frontier Software

Increase unknown ID throughput and confidenceKnow your unknownsFrom spectra to structureBuild, store, share and leverage your knowledge
Take control of your unknown small molecule identification challenges and make use of comprehensive libraries, fragmentation tools, reporting and curation tools – turning your data into knowledge.Automate complex sample deconvolution and library searching to identify your unknowns using the world’s largest and highest quality mass spectral library.From infusion or LC-MS, nominal or high resolution data, take high quality MSn data and deliver results; even with no library hit, fragmentation information and leading algorithms provide you with actionable results.Explain your identifications through fragmentation or reaction pathways, with the ability to build and share proprietary libraries to leverage your knowledge.

Learn more about how Mass Frontier Spectral Interpretation Software works


Covering a wide range of small molecule applications, the extensive structural and chemical diversity of mzCloud, ensures absolute confidence in any unknown identifications.

Making use of exhaustive high-resolution MS/MS and multi-stage MSn spectra, combined with extensive metadata, the world's largest (in terms of total spectra and data per compound) and most extensively curated mass spectral library delivers powerful unknown identification capabilities.

Identify more unknowns with MSn and SubTree search

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.

How was the world's largest mass spectral fragmentation library, mzCloud, created?

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

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
A representation of the MS2 vs MS2 identify search, which compares MS2 spectra from the query tree to MS2 spectra from mzCloud or a reference library to identify compounds

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.

A representation of the MSn vs MSn tree search, which searches any of the Query MSn trees against mzCloud or the reference library

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.

A representation of the identity substructure search (MSn vs MSn), which allows you to make use of any extensive substructural information when there are no exact matches available within the queried library

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.

A representation of the subtree search (MSn vs MSn), which seeks to match substructures from the library based upon MSn spectral matching

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.


What happens when you don't get a match from your library search? You can still utilize the comprehensive fragmentation information contained within mzCloud! Through spectral similarity and sub-structural information (precursor ion fingerprinting), mzLogic can take all of this information and provide you with the best candidates for your true unknowns.

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When small molecule unknowns don't provide a spectral hit, how can we still identify them?

Maximize your real fragmentation data by combining spectral library similarity searching with chemical database searching.


For the creation, editing and searching of reaction pathways, the new Metabolika module means you can take your knowledge to the next level. With publication quality graphical functionality to create and edit reaction pathways, and more than 370 curated and annotated biochemical pathways for a range of organisms already included, it is easier than ever to share your pathway knowledge.

Metabolika Module is also utilized within substructure searching, fragmentation prediction and for mzLogic, further increasing the chances of unknown compound identification.

Example of an included Matabolika biological pathway

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

Automated fragmentation annotation and understanding

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.

A representation of a FISh analysis which can filter structurally similar compounds and automatically localize the modification site and label and apply color-coding to fragments common to both the parent and filtered results

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.


With the ability to create, curate and share your libraries, and therefore knowledge, comes the power to really share your insights across your organization. Curator allows you to use the same tools that curate mzCloud to create your own high quality mass spectral libraries; these libraries are easily managed within Mass Frontier’s Data Manager, with this knowledge being shared across your network with the included Server Manager.

Curated spectral record – local mzCloud

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.

Ordering guide for Mass Frontier Spectral Interpretation Software

Connect your lab to drive more insights from your data

Connect your lab to drive more insights from your data

Small molecule characterization and identification clouding your decision making? Cloud-based technologies, including mass spectrometry analysis software, are becoming more prevalent in laboratories.

Related applications and technology


Additional resources

Style Sheet for Global Design System
CMD SchemaApp code