Identify any Spectrum with Our NIST Library Upgrade

Sherlock Holmes had his magnifying glass—but he also had a mental “library” of items with which he could compare what he saw. If not, he wouldn’t have solved many crimes.

Today, research lab technicians (who are sometimes real crime stoppers!) use mass specs to help solve scientific puzzles. Since there’s no way to hold hundreds of thousands of compound spectra in your head—this is where the NIST library upgrade becomes invaluable.

When identifying an unknown spectrum, experienced lab techs might be able to get a read on the basic type of compound—but narrowing it down requires more. This is the value of the NIST library upgrade: It provides multiple factors for accessing an extensive library of known spectra—including almost 25,000 new compounds.

The NIST Mass Spectral Library provides not just one, but three different factors to identify unknowns.

The Match Factor

The Match Factor is a numeric value between 1 and 999 that results from a comparison of the sample spectrum and the library spectrum that is the “Hit.” This value takes into account a comparison of the peaks (m/z values and their relative intensities) in both spectra. The number is lowered if there are peaks in the sample spectrum that are not in the library spectrum and if there are peaks in the library spectrum that are not in the sample spectrum.

If you search the NIST Library called “mainlib” (only a single spectrum for each compound) and the NIST Library called “replib” (replicate spectra of compounds in the mainlib that are often encountered in various GC/MS analyses, like solvents, pesticide, food additives, toxins, etc.), and get multiple hits for a single compound, then there is a higher probability that you have identified the compound if match factor values are >750. You can also check the CAS Numbers of the listed compounds to verify identity.

The Reverse Match Factor

The Reverse Match Factor is calculated by disregarding any peaks in the sample spectrum that are not in the library spectrum. This is to account for co-elution. If you have done a good job of background subtraction, then the Match Factor and Reverse Match Factor values will be very close.

Probability Factor (Prob)

Use caution when using Prob, which is a very complicated value. It has to do with whether or not the spectrum for that compound has similar spectra in the library. For example, if you search the spectrum Fluometuron (CAS# 2164-17-2) from the NIST mainlib against the NIST 14 mainlib and replib, the Prob value will be 98%.  However, if you search the spectrum of m-Xylene (CAS# 108-38-3), you will get a Prob value of only 62%. This is because the spectrum for m-Xylene is very similar to the spectra of o-xylene, p-xylene, and ethylbenzene: whereas there is no other spectrum in the database that is similar to the spectrum of Fluometuron. The bottom-line is that you have to be very careful with relying on the Prob value.

AMDIS (Automated Mass Spectrometry Deconvolution and Identification System)

Your best results will be achieved if you process data files through the AMDIS utility provided with the NIST Mass Spectral Library. AMDIS has been designed to reconstruct “pure component” spectra from complex RTIC chromatograms even when components are present at trace levels. It is installed when the NIST MS Search and Database are installed. Send the deconvoluted spectrum from AMDIS to the NIST MS Search Program.

AMDIS can also be used to assign Retention Indexes to the sample spectrum which will allow the use of the NIST RI Database.

Other important factors to keep in mind:

Keep in mind that different spectra, of the same compound may appear different in the NIST database due to methods of sample introduction. A huge amount of human effort has gone into the review of the spectra in the NIST DB; however, we still find differences that need to be judged.

Another factor has to do with the fact that the NIST 2017 Mass Spectral Library has EI mass spectra for over 267,000 compounds. The NIST 2017 Retention Index (RI) Database has Retention Index values for over 99,000 compounds. There are only spectra for 72,000 of the compounds in the RI DB that are in the EI DB. There are a lot of compounds that do not have spectra in any database.

Finally, an important aspect of identification of unknowns is whether the spectrum makes sense. You will need to study interpretation of mass spectra to determine this. There are a number of books and courses that can help. Check out the mass spectral interpretation courses at

To learn more about the NIST library upgrade benefits, visit this post or contact us today at 888-669-1233.