7.2: Sources of Spectral Data

AIST Spectral Database for Organic Compounds (SDBS) - http://sdbs.db.aist.go.jp

This database from Japan has a wealth of spectral information and is the best for searching, as there are many options to find what you need. Sadly, the majority of the spectra are presented as image files only (no JCAMP-DX) with only numeric peak data for MS and 1-NMR spectra (click the ‘peak data’ button. Currently, the site has the following amounts of spectral data:

MS: ~25000 spectra
1H NMR: ~15900 spectra
13C NMR: ~14200 spectra
FT-IR: ~54100 spectra
Raman: ~3500 spectra
ESR: ~2000 spectra

NIST Chemistry Webbook - http://webbook.nist.gov/chemistry/

The NIST Webbook is a prime source of spectral information about small organic compounds available as JCAMP-DX files, Scalable Vector Graphic (SVG - http://www.w3.org/Graphics/SVG/) files (an image format specified in XML), png image files, and scans of the original data (some from the 1960s). Searching for spectra on the site is done via the compound search and selection of the spectral data to be returned (if it is available for the compound(s) found). Other information such as thermodynamic property data, gas chromatograms (linked to original journal papers), and vibrational and electronic energy levels is also available on the site. Currently, the site has the following of spectral data:

IR spectra for over 16,000 compounds
Mass spectra for over 33,000 compounds
UV/Vis spectra for over 1600 compounds


7.2.1: ChemSpider Spectra Search

ChemSpider has over 10,000 spectra associated with chemical compounds in its database. Some of these are from commercial companies and organizations, but a large number have been uploaded by users of the website. As a result there may be spectra for compounds that are not available elsewhere. You will find that the spectra are available sometimes as JCAMP files ( in which case you can open them in the browser and interact with the spectrum using the embedded display tools - available as both Java and non-Java options) and other times users have provided pdfs, or image files( jpg, png etc).

In addition to the spectra that are available within ChemSpider, some records provide links to other sites that have spectra data not available in the ChemSpider database, such as NMR ShiftDB and the  NIST Chemistry WebBook.

It is also possible to get some information about spectra using one of the sites API’s (see below), which you need to create an account (free) to use. Access the following URL to get an XML file that lists all current spectral data by entering your security token in the ‘token’ field, which can be found on the http://www.chemspider.com/UserProfile.aspx page once you login on the ChemSpider website.

Finding spectra in ChemSpider records

There are tools to help you find ChemSpider records that have "Analytical data" - this term is used to encompass any of the following types of data: NMR, IR, UV-Vis, MS and Crystal structure. The option to return on but provide an option to filter results according to whether they have analytical data (this includes IR, MS, NMR, UV-vis and Crystal structures). This option is available by clicking on the Filter button that is available on of the search pages (SimpleStructureAdvanced) - but not on the quick search boxes that are provided on the homepage or in the header bar and then checking the the Filter only those having analytical data option.

The Filter options

While you can use this option in any search you should think carefully when performing exact searches: try searching for ubiquinone with the Filter only those having analytical data option checked and unchecked.

By contrast, the Filter only those having analytical data option works well with queries that are expected to return many results, for instance searching for all records which have a name that contains the substring hydroquinone (hint: use *hydroquinone* as the search string). In fact, using the Advanced search page you can add the filter to any of the searches, opening up the ability to search by, Molecular formula, Average mass, predicted properties etc. and see records which have some analytical data (but do remember that this filter can return records that have crystal structures but no spectra). 

Finding spectra in other resources from ChemSpider records

ChemSpider can also help users identify other resources that might have spectra data that are not available in ChemSpider itself.

If you look at the Data Sources tab (you often need to use the More dropdown to access this) in a record (eg Malonic acid - http://www.chemspider.com/Chemical-Structure.844.html) we have links to lots of other useful resources, you don’t have to scan through all of these to find useful data, there are sub-headings that display sub-sets of data sources according to their classification. Two relevant headings are Xtal structures (short for crystal structures) and Spectral data which list other websites and databases that have spectra data for that compound.

The data sources tab showing the Spectral data classification subset

Where possible the external id will act as a link to the record on the external resource.

 

Filter a ChemSpider search to find only records that reference a (spectral data) datasource

You can actually use the ChemSpider search interface to find data in one or more of the data sources that we agregate. This means that you can specify that a search only returns records that are listed as being in MassBank.  For example, from the Advanced search page you can use the Data source  Data source interface and check only the MassBank data source (you can actually check as many data sources as you wish). You can also select a to restrict your search to one or more classes of data source. Eg Spectroscopy databases (just a different label for the data sources that appear under the Spectral data sub-heading) found under Data Source  Data source typeThe interface for restricting search results according to data sources

The data source selection options can be combined with other search parameters.

Eg. Identifier (substring) = *yohimb* and Data source type = Spectroscopy databases,

or  monoisotopic mass = 104.01095 +/- 0.005 and Data source = MassBank

However, the one thing to remember is that the data in ChemSpider is only as recent as the last update provided by the data sources - so there might be cases where data that can be found by searching the individual databases is not found in a search on ChemSpider because it was added to the indivudual data base after the  last update supplied to ChemSpider.


ChemSpider - http://www.chemspider.com

ChemSpider has over 10,000 spectra associated with chemical compounds in its database. Some of these are from commercial companies and organizations, but a large number have been uploaded by users of the website. As a result there may be spectra for compounds that are not available elsewhere. Finding compounds that have spectra available is not easy to do and in fact you can only access this information via one of the sites API’s (see below), which you need to create an account (free) to use. Access the following URL to get an XML file that lists all current spectral data by entering your security token in the ‘token’ field, which can be found on thehttp://www.chemspider.com/UserProfile.aspx page once you login on the ChemSpider website.

http://www.chemspider.com/Spectra.asmx?op=GetAllSpectraInfo

You can also search for spectra using the other commands on the http://www.chemspider.com/Spectra.asmx page, and search the mass spectra using commands found in the MassSpecAPI page at http://www.chemspider.com/MassSpecAPI.asmx. For example to search for peaks in a mass spectrum of mass 1000 ± 0.1 you can go to (no token required):

http://www.chemspider.com/MassSpecAPI.asmx/SearchByMass2?mass=1000&range=0.1

Other Sources of Spectra

NIST Atomic Spectra Database - http://www.nist.gov/pml/data/asd.cfm
NIST Molecular Spectra Databases - http://www.nist.gov/pml/data/molspec.cfm
NMR Shift DB - http://nmrshiftdb.nmr.uni-koeln.de/
Human Metabolome Database - http://www.hmdb.ca
EPA Emissions Measurement Center Spectral Database -http://www3.epa.gov/ttn/emc/ftir/index.html
MassBank - http://www.massbank.jp/
Romanian Database of Raman Spectroscopy - http://rdrs.uaic.ro/index.html

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Comments 2

OLCC s12's picture
OLCC s12 | Tue, 11/03/2015 - 23:02
I went to the ChemSpider Spectral page that was listed in this section to access all of the spectral data and it did not work after entering my token. Im interested in seeing how the response code looks in the API service. Would this be something that may need to be approved by the site administrators to use? Seems like it may use a lot of server resources in calling this API.

Bob Belford's picture
Bob Belford | Wed, 11/04/2015 - 16:23
All, In response to this comment David Sharpe of RSC has added a bit to this module on ChemSpider Spectra searches that I think everyone should look at, play around with, and comment on. Although it is embedded into this page, you have to click on the link 7.2.1:ChemSpider Spectra Search to see the full post, and comment directly on it. Here is the direct link, <a href="http://olcc.ccce.divched.org/2015FallOLCCM7P1TLO5">http://olcc.ccce.divched.org/2015FallOLCCM7P1TLO5</a> Cheers, Bob

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