mzCloud Mass Spectral Library

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.

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.

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.

Learn more about mzLogic

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.

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.

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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