Mass Spectra Databases

MassBank. MassBank was the first mass spectra database of small chemical compounds for life sciences (<3000 Da) (MassBank, 2016). This repository was designed to share the obtained mass spectral data among the scientific community (Horai et al., 2010, p. 703). Thus, MassBank data could be useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry. Among other features, MassBank supplies (1) tandem mass spectra acquired on broad range of mass spectrometers as well as different ion sources; (2) a friendly interface, which could be used to find mass spectrum by chemical name or molecular formula; and (3) an easy way to search similar spectra on a neutral loss-to-neutral loss basis.

Chemspider. ChemSpider is a free online service that delivers information of more than 57 million structures from hundreds of data sources (Chemspider, 2016). These sources include data from government databases, commercial chemical supplier catalogs, academic and commercial website. Thus, it could be considered as the richest single source of structure-based chemistry information. For identification purposes, ChemSpider is useful to obtain MS and MS/MS spectra from known compounds. The spectra can only be found by systematic name, trade name, SMILES, InChI, or CSID. However, it is not possible to obtain information of compounds, which have not been partially identified before.

METLIN Metabolomics Database. This web-based database has been developed by the Scripps Research Institute (California, USA) (METLIN, 2016). This database is designed to provide, among others, structural and physical data on known endogenous metabolites, drugs, and pesticides and their metabolites and high-accuracy mass spectrum data from known compounds and their derivatives (Smith et al., 2005, p. 747). In addition, a wide MS/MS spectra collection has been developed. This information has been obtained on an Agilent 6510 Q-TOF instrument by collecting compound-specific reference spectra at three different CEs. The mass spectrometer is operated in both ESI positive and negative modes. Currently, there are more than 700,000 high-resolution MS/MS spectra available. It should be noted that this number is continuously expanding.

A new database namely isoMETLIN has been developed through METLIN (Cho et al., 2014, p. 9358; IsoMETLIN, 2016). This database could facilitate the identification of metabolites that have been isotopically labeled. Thus, in the field of pesticide analysis it could be a powerful tool, as the number of isotope labeled species is gradually increasing. This database allows to search all computed isotopologues derived from METLIN on the basis of m/z values and specified isotopes of interest, such as ¹³C or ¹⁵N. In addition, isoMETLIN provides experimental MS/ MS data on hundreds of isotopomers.

The Spectral Data Base for Organic Compounds. The Spectral Data Base for Organic Compounds (SDBS) (2016) is a free online site developed by National Institute of Advanced Industrial Science and Technology in Japan. SBDS contains six different types of organic compounds including an electron impact mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a ¹H nuclear magnetic resonance (NMR) spectrum, a ¹³C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum. This database has more than 25,000 MS spectra, which were obtained by the electron impact method.

Human Metabolome Database. The Human Metabolome Database (HMDB) is an online database of small molecule metabolites found in the human body. This freely available electronic database contains detailed information about 42,000 small molecule metabolites. The project has been developed by the Canadian Institutes of Health Research, Alberta InnovatesdHealth Solutions, and by The Metabolomics Innovation Centre (Human Metabolome Database, 2016). This database was designed to give helpful information about (1) chemical data, (2) clinical data, and (3) molecular biology/biochemistry data. In the field of mass spectrometry, to identify or characterize human metabolites, HMDB allows to query NMR spectroscopy, GC MS spectrometry and LC/MS spectrometry data. In fact, HMDB includes nearly 10,000 NMR, GC MS, and LC/MS spectra. Additionally, there are other databases related to HMDB including Urine Metabolome, DrugBank, Toxin and Toxin Target Database (T3DB), Small Molecule Pathway Database (SMPDB), and Food Database (FooDB). The HMDB provides information about 3100 small molecule metabolites found in human urine (Urine Metabolome Database, 2016). Up to date, the DrugBank database (Drugbank, 2016) helps to get information about more than 8200 drug and drug metabolites. T3DB (Toxin and Toxin Target Database, 2016) contains information on 3673 toxins such as pollutants, pesticides, drugs, and food toxins. SMPDB (Small Molecule Pathway Database, 2016) has more than 618 pathway diagrams. FooDB is the most recent database in HMDB site (Food Database, 2016). This database contains information on 28,000 food components and food additives. Among others, FooDB allows to obtain data on (1) MS and MS/MS spectra, (2) nomenclature, and (3) concentrations in various foods.

Fiehn Library. This database has been developed by West Coast Metabolomics Center (California, USA) (Kind et al., 2009, p. 10,038). The library has been developed using several mass spectrometers including TOF or single quadrupole using electron impact ionization. Currently, this database contains over 1000 identified metabolites. MS spectra along with retention time allow to obtain a comprehensive metabolic profiling.

mz Cloud. mz cloud is a free database, which contains information on 6000 compounds and more than 1,518,041 high-resolution MS/MS spectra (m/z Cloud Database, 2016). This spectra information is shown to the user with spectral trees. Thus, the users could find the information in a more intuitive way. Most data displayed have been collected with Thermo mass spectrometers. MS/MS and multistage MSn spectra were acquired at different CEs, precursor m/z, and isolation widths using CID and HCD. mz Cloud provides information about (1) the chemical structure, (2) computationally and manually annotated fragments (peaks), (3) identified adducts and multiply charged ions, and (4) molecular formulas, predicted precursor structure. Additionally, mz cloud will allow registered users to create individual, public, or private spectral libraries increasing the laboratory workflow.

A summary of mz cloud interface work is illustrated in Fig. 2.16, on the search of MS-spectra information of dopamine. First of all, the user should indicate the compound name (Fig. 2.16A). In this section, additional complementary information for instance related to the mass spectrometer and ionization mode used is available. Then, the user can select the different MSn spectra available in the spectral tree (Fig. 2.16B). Finally, parameter such as CID or HCD applied in the selected MSn spectrum could be checked.

The following databases are not readily available. However, because of their wide use and acceptance by scientific community it is worthwhile mentioning them. These databases are the Wiley Registry MS/MS and the NIST MS/MS database.

The Wiley Registry MS/MS. This MS/MS spectral library includes nearly 775,500 MS/MS spectra and 741,000 chemical structures. Thus, sensitive, specific, and robust identification of small molecules such as illicit drugs, pharmaceutical compounds, pesticides, and other small bioorganic molecules could be carried out (Oberacher, 2013, p. 312). These MS/MS spectra were obtained with different high-resolution mass spectrometers (Q-TOF) employing positive or negative ESI at least at 10 different CEs (Wiley, 2016). Its full potential has been checked in several cross-validation studies using sample spectra extracted from tandem mass spectral libraries from literature and acquired on various types of tandem mass spectrometers (Oberacher, Whitley, & Berger, 2013, p. 487).

The NIST MS/MS database. This database was developed by National Institute of Standards and Technology (NIST, Maryland, USA). NIST MS/MS database, which is widely used for scientific community, is supplied by John Wiley and Sons (NIST Standard Reference Database, 2016). The aim of this library is to provide reference mass spectral data for the identification of compounds through the fragmentation of their ions generated by ESI. MS spectra were obtained using several types of mass spectrometers, including low- and high-resolution mass spectrometers, including ion trap, QqQ, and Q-TOF. ESI electronic impact ionization has been employed. NIST MS/MS database currently provides more than 193,119 and 41,165 MS/MS spectra of small molecules and biologically active peptides, respectively (NIST Standard Reference Database, 2016).