mzCloud Mass Spectral Library

Confident identification for unknown small molecules

Mass spectral libraries and databases may be required to identify unknown compounds when reference standards are not available. This is particularly true for studies in areas such as metabolomics, forensic toxicology, food & beverage, environmental emerging contaminants or extractables & leachables.

In these situations, a mass spectral library, particularly a high-resolution and accurate-mass MSn fragmentation library, such as the mzCloud mass spectral library, can provide the information required to confidently identify unknown compounds.

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Key benefits of the mzCloud mass spectral library

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 to provide confidence in your results.Identify unknowns with automated deconvolution and library searching against extensive fragmentation spectra covering a wide chemical space, including small molecule applications.With solutions to cover infusion or LC-MS, 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 the Thermo Scientific Compound Discoverer and Mass Frontier software packages. Not online? mzVault provides you with the ability to perform offline spectral library searching.

Learn more about the mzCloud mass spectral library

Discover the difference that high-resolution mass spectral libraries can make when addressing the challenges of small-molecule unknown characterization and how powerful data analysis tools can make the most of these libraries by allowing you to find answers quickly and confidently to drive your decision-making process.

mzCloud is an extensively curated, high-quality mass spectral fragmentation library that contains significant amounts of spectra and metadata for each entry. Each entry also includes exhaustive high-resolution MS/MS and multi-stage MSn spectra, which have been acquired at various collision energies and using different fragmentation techniques.

Each raw mass spectrum has been filtered to remove noise, recalibrated to ensure absolute mass accuracy, fully annotated and curated to ensure quality and consistency.

Finally, the contents of the library are updated weekly to provide coverage of a wide chemical space, ensuring relevance to all small-molecule application areas.

Mass Frontier software with mzCloud

Example of the Mass Frontier software utilizing the contents of mzCloud to identify an unknown compound through a sub-structural search; the experimental fragmentation spectrum (top left) is searched against the mzCloud mass spectral database, with corresponding spectral hits shown in a given spectral tree (top, middle), with supporting spectral information (bottom left) and the identified precursor structure from the matched fragmentation spectra (bottom right), and the library compound structure from which the fragment originated (top right).

Distinguishing among types of databases is important, as the contents and quality of the contents typically differs significantly and may have an impact upon the reliability of the data and the confidence in any results obtained.

  • Chemical database: A collection of chemical information with, at minimum, a name and a formula. It may also include structures, elemental composition, retention time information, and additional biological or chemical metadata.
  • Accurate-mass (AM) database: An AM database contains accurate mass formulas.
  • Accurate-mass retention-time (AMRT) database: An AMRT database contains accurate mass and retention time(s) for specific analytical methods.
  • Library: A library is a database (AM or AMRT) that, in addition to the above, also contains reference mass spectral data, MS/MS, and/or MSn data on compounds.
mzCloud spectral tree

A schematic representation of a spectral tree within 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.

mzCloud is an all-encompassing mass spectral library with content based on a wide chemical space (therefore covering all small-molecule application areas), and acquiring high-resolution and accurate-mass data at various collision energies, for multiple adducts, using CID and HCD. Approximately 10–20 collision energies are included for every precursor ion; this multi-stage, multidimensional MSn spectral data are arranged into spectral trees, which are both extensive and comprehensive, typically containing many hundreds to thousands of spectra for each compound, with many exceeding MS4 fragmentation steps.

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. Additional tools in Compound Discoverer and Mass Frontier software, including mzLogic, use the extensive fragmentation information to confidently identify unknowns that cannot be identified based upon the spectral library compound entries alone.

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mzCloud content curation tool

An example of the mass spectral content curation tool available within the Mass Frontier software. It contains all the functionality used to manually curate the content contained within mzCloud. The power of mzCloud lies in both the extent and high quality of its content, which helps make confident compound identifications.

Despite the fact that Thermo Scientific Orbitrap-based mass analyzers routinely deliver sub 3-ppm mass errors, there is a small amount of inaccuracy in any experimental data used to search against a library; these errors would be compounded if the library itself also contained data with mass errors. The compounded errors would mean that any identifications could be harder to make or have lower confidence due to match scores being higher.

Curating the content within mzCloud guards against error and variability in the reference spectra against which data is compared. The process of curation involves:

  • Averaging multiple, individually acquired spectra
  • The removal of mass spectral noise
  • Recalibration of the mass spectra based upon the predicted formulas for the fragment ion elemental compositions, based upon the known elemental composition and structure of the precursor ion
  • Annotation of all fragment ions with the fragment structure
  • Addition of large amounts of metadata, including the source of the data and all original raw data files

This curation process is performed for every spectra — every collision energy, every fragmentation type, every MSn level and for each precursor ion. As such, the spectral data in mzCloud is of exceedingly high quality and offers significant advantages over crowd-sourced libraries due to the high levels of control.

Recalibrated fragmentation spectrum

A recalibrated fragmentation spectrum showing no error on the highlighted peak at m/z 213.05462, along with all of the annotation that is provided for each spectra, at each collision energy, for each fragmentation type at each MSn level.


Accelerate your small molecule unknown identification studies with mzCloud, mzLogic, and the other data analysis and mass spectral prediction tools available in Compound Discoverer software and Mass Frontier software.

The content within mzCloud is accessible through Compound Discoverer and Mass Frontier software packages, provided you have an internet connection. No internet? No problem – mzVault, provides you with the MS and MS/MS content of mzCloud in an offline format.


Due to security concerns or local firewalls, not everyone can connect processing PCs to the internet. With that in mind, the contents of mzCloud are combined into an offline version twice a year. The mzVault software application helps you access this information. In addition to accessing the offline version of mzCloud, the mzVault application can store and search your high-quality custom in-house (offline) MS/MS spectral libraries.

mzCloud, which still provides a superior solution for the identification and characterization of unknowns, as well as allowing you to utilize the many tools in the Compound Discoverer software and Mass Frontier software.

Even when complex samples give rise to complete unknowns that do not match any compound in mzCloud, or when there are too few identified fragments to make a putative identification, the ability to store this information in a custom library allows users to search the data to see if an 'unknown' has previously been observed, thereby building up a repository of useful information. Compound Discoverer software allows you to send your mass spectral data to an existing mzVault, or to create a new one, and the Mass Frontier software contains the curation tools required to bring any mzVault library created to the same standard as mzCloud.

Download the offline mzVault for mzCloud MS2

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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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In this webinar we discuss a fundamental new approach to untargeted small molecule analysis involving optimized mass spectrometers, powerful new data acquisition strategies, and an arsenal of new software tools to translate high-quality Orbitrap mass spectra into more, confidently-assigned small molecule structures.

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