Mass Spectral Libraries

Identify more through libraries and knowledge stores

Mass Spectral libraries and databases provide the opportunity to automatically analyze large amounts of MSn data and identify many small molecule components, as well as transferring knowledge from research into more routine, quantitative applications. However, analysts require certainty for unknown identifications, which means that libraries, databases and knowledge stores must contain high-quality, accurate data.

Find out more about what it takes to deliver confidence for unknown identification, even when there is no hit within a spectral library, or how to curate your own high-quality library to share your knowledge.

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Discover the difference that high-resolution mass spectral libraries make to addressing the challenges of small-molecule unknown characterization, and how powerful data analysis tools can make the most of these libraries.

Small molecule identification is challenging, especially for many applications where reference standards are not available or easily accessed. Comprehensive mass spectral fragmentation libraries can provide the necessary confidence to identify compounds through a spectral match, fragment ion match, isotopic patterns or even ratios of fragment ions.

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.

Each mass spectrum has been filtered, recalibrated, averaged and fully structurally annotated. In addition to this high-quality data, each MSn fragmentation spectra have been acquired at various collision energies, for multiple adducts, with collision induced and higher energy collisional dissociation. The power of mzCloud comes alive when combined with mzLogic.

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Key benefits

Confidence for unknown identificationKnow more unknownsFrom spectra to structureFlexibility for research and routine applications
Comprehensive curation of all library content, with extensive, fully annotated and searchable fragmentation spectra, provide confidence is your results.Identify unknowns with automated deconvolution and library searching against extensive fragmentation spectra covering a wide chemical space, and therefore small molecule applications.With solutions to cover infusion or LCMS, nominal or high-resolution data, you can be sure that your MSn spectra will provide you with actionable results, even when there is no spectral library match.Search for free online at, or directly access through Compound Discoverer and Mass Frontier. Not online? mzVault provides you with the ability to perform off-line spectral library searching.
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.

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

Search extensive online structural libraries using confident elemental compositions to return potential structures. Even if you have hundreds or thousands of candidates, mzLogic will fully utilize your high-quality MSn spectral data to identify common sub-structural information from the extensive mzCloud spectral library.

This sub-structural information is used to rank the candidates and create a significantly smaller list by comparing the amount of common substructure overlap. This process can be fully automated within the Compound Discoverer software. For even greater confidence, the Mass Frontier software provides you with a deep understanding of the fragmentation mechanisms of your reduced candidate list to increase certainty in any putative identification.

Key benefits

Combine the benefits of multiple libraries and databasesTake the guesswork out of unknown identificationGo from thousands of potential candidates to a handful
From mzCloud, the most extensive mass spectral fragmentation library, to numerous online structural databases, mzLogic can combine the contents to aid in unknown structural identification.Even if there is no match from mzCloud, the extensive fragmentation information can still be used to identify common sub-structural information from your MSn data, aiding in putative identification.Using elemental composition to search structural databases can return thousands of potentials; mzLogic uses your MSn data and the full mzCloud fragmentation library to explain as much structural information as possible to reduce thousands of potentials to a handful based upon structural similarity.
mzLogic algorithm and the high quality, structurally diverse mass spectral fragmentation information

Take the guesswork out of small molecule unknown identification through the combination of mzLogic algorithm and the high quality, structurally diverse mass spectral fragmentation information contained within mzCloud, to propose and confirm structural identification.

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Discover how mzLogic helps you to automate the process of identifying your true unknown unknowns when there is no spectral library match. Maximize your real fragmentation data by combining spectral library similarity searching with chemical database searching to rank and confidently propose the most likely candidate.

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

Your data has inherent value, as it is the knowledge that you acquire. mzVault provides you the capabilities to access and search mzCloud’s MS2-level spectral data off-line, or to store your own spectral library information. Spectral information, and your knowledge, can be automatically sent from Compound Discoverer into a new, or existing library which can then be searched using Compound Discoverer or Mass Frontier.

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When you need to curate proprietary libraries and ensure the highest quality data, Mass Frontier provides you with the same tools used to curate mzCloud, meaning that you can ensure your spectral data has been filtered, recalibrated, averaged and fully structurally annotated, ready to share your knowledge within your organization.

Key benefits

Know more unknowns off-lineCreate and share your knowledgeHave I seen this unknown before?Curate your high-quality data
Sometimes it isn’t possible to be online and access mzCloud. mzVault contains all MS2-level spectral data contained within mzCloud to allow for confident unknown identifications.Create, store and search your own in-house spectral libraries. Once you have identified unknowns through mzLogic, or you have your proprietary compounds, make sure that this valuable information can be leveraged.Even with extensive online structural databases, and mzLogic to propose a structure or sub-structure, there can be occasions where it remains an unknown. Store this information and re-use to see if you have previously observed any unknowns.When it is important to curate your valuable data, the Curator tool from Mass Frontier allows you to use the same tools used to populate mzCloud, ensuring the creation of your own high-quality mzVault proprietary libraries.

Create, edit and search reaction pathways using the new Metabolika module to take your knowledge to the next level. With publication-quality graphical functionality to create and edit reaction pathways within Thermo Scientific Compound Discoverer 3.0 or greater, and Thermo Scientific Mass Frontier Software 8.0 or greater, and more than 370 curated and annotated biochemical pathways for a range of organisms, it is easier than ever to share your pathway knowledge.

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

When used within the Compound Discoverer software, this module can take your data visualization to a new level with interactive statistical data overlay, including metabolic flux analysis data.

Key benefits

Create, edit and store reaction pathwaysAccess knowledge of >370 metabolic pathwaysMap pathways to your data, as well as visualize your statistical information
From the included >370 metabolic pathways, through to your own reaction pathways, easily curate and edit your knowledge for future use within both the Compound Discoverer and Mass Frontier software.The combined knowledge of the included pathways isn’t just restricted to Metabolika, the information is also fully utilized for substructure searching as well as with mzLogic.Pathways can be easily mapped to your detected compounds within the Compound Discoverer software, with highly visual and interactive representation. Additionally, your statistical information from flux analyses can be displayed within Metabolika pathways for easy data visualization.
Example of Metabolika pathways analysis tool with flux analysis data included

An example of Metabolika pathways analysis tool with flux analysis data included, showing qualitative flux analysis of exchange rates from a stable isotope labeling experiment.


With the ability to create, curate and share your libraries within Thermo Scientific Mass Frontier 8.0 or greater comes the power to share your insights across your organization.

The Curator feature of the Mass Frontier software allows you to use the same tools that curate mzCloud to create your own high-quality mass spectral libraries. Supplement your knowledge with full precursor and fragment ion structures and formulas, with mass recalibration, adduct detection and annotation, as well as collision energy breakdown curves for your own MSn spectral trees.

Your libraries are easily managed within the Mass Frontier software Data Manager, with this knowledge being shared across your network by the included Server Manager.

Key benefits

Store your knowledge and access its valueCreate the highest quality mass spectral fragmentation librariesFully annotate your data, as well as include informative metadata
Your data has value, it is the knowledge and information that you gather to help make informed decisions. Curator ensures that you can capture and fully utilize your data, your knowledge, and access its true value.Ensure that your data is the highest quality by creating your spectral trees through using the same tools which are used to curate mzCloud; remove noisy spectra and artefacts as well as fully recalibrate your data.Complement your high-quality mass spectral fragmentation data with full structural and formula annotation of precursor and fragment ion peaks, with collision energy breakdown curves as well as metadata retrieval from public sources.
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.

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.

Evaluate for free, order now or upgrade your software

Download a free 60-day trial to discover for yourself how Compound Discoverer software and Mass Frontier software can harness the power of mass spectral libraries and unknown compound analysis tools, as well as numerous other valuable tools to get the most out of your data.

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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.

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