Spectral Information in PubChem

Did you know that a growing number of chemicals in PubChem contain spectral information?

There are now more than 300 thousand chemicals with spectral information available, including 13C NMR, 1H NMR, 2D NMR, ATR-IR, FT-IR, GC-MS, Raman, UV-Vis, vapor-phase IR, and more.  This content comes primarily from four data sources: the NIST/EPA/NIH Mass Spectral Library, the Hazardous Substances Data Bank (HSDB), the Human Metabolome Database (HMDB), and a new addition, SpectraBase.

The NIST/EPA/NIH Mass Spectral Library includes images of the top-three peaks of GC-MS or MS-MS spectra along with related metadata and annotation for more than two hundred thousand chemicals. The Library’s annotation includes instrument, collision energy, spectrum type, and associated metadata information.

HSDB content is text-based and includes citations and spectra peak information for thousands of chemicals. HMDB annotation includes links to spectra for thousands of chemicals.

PubChem Spectral_data

SpectraBase, provided by Bio-Rad, a commercial publisher of spectral databases and spectroscopy software, includes images of, annotation about, and links to a diverse set of spectral information for tens of thousands of compounds. SpectraBase content includes extensive annotation and a variety of metadata, such as the instrument, measurement technique, sample source, and spectrum source, in addition to the image of the spectra.

For all four sources, additional spectral information is often available directly from the source and easily accessed using the links on the PubChem page.

 

How to find and access spectral data for a compound?

PubChem records with spectral data have a Table of Content (TOC) section labelled “Chemical and Physical Properties” with a “Spectral Properties” subsection. One can use the TOC to jump to a given type of spectral data content.  Clicking the SpectraBase image or the HMDB link directs the user to an external web page for that compound, where one can further interact with the spectral information.

PubChem Classification Browser

The PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72) can help you locate all PubChem Compound records containing a particular type of spectral information.  The “Spectral Properties” node can be found under the “Chemical and Physical Properties” section in the PubChem Compound Table of Contents (TOC) classification tree.

PubChem presents at the 254th American Chemical Society National Meeting in Washington D.C. (August 20-24, 2017)

On August 20-24, 2017, the 254th American Chemical Society National Meeting will be held in Washington D.C.  The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem.  Below is a list of presentations that will be given by the PubChem staff.

 

Day 1 (Sunday, August 20)

 

Day 2 (Monday, August 21)

 

Day 3 (Tuesday, August 22)

  • CINF108: PubChem and open data (S. Kim)
    Junior Ballroom 2 – Washington Marriott at Metro Center, 5:00 pm – 5:25 pm

 

Day 4 (Wednesday, August 23)

 

Day 5 (Thursday, August 24)

 

In addition, one of PubChem’s collaborators will give a presentation on our joint effort to develop a new service that provides information on biologics.