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NIST Library

Posted: Sun Jan 20, 2019 5:54 am
by M.John
Hi all,
Does anyone know why the structure of identified compound is not shown on "spec list" in NIST library? I have "?" instead of the structure (please see the picture below)


Image

Re: NIST Library

Posted: Sun Jan 20, 2019 3:20 pm
by Consumer Products Guy
As someone who actually "built" two Agilent search libraries for my company by injecting standards, my guess is that the pattern for methyl palmitate did not have a structure entered in for that entry.

I see your software matched your peak with methyl palmitate, so not sure I understand the question.

In the early days of GCMS search libraries (1990s), it was not uncommon for purchased NIST libraries to have such omissions.

Re: NIST Library

Posted: Mon Jan 21, 2019 5:12 am
by M.John
Yes, the software matched my peak with methyl palmitate, but my question is why the chemica structure of methyl palmitate is not shown in "spect list" (spect list is the upper pane in the left side) and as could be seen, no structure is shown. Instead, "?" is appeared.

Is there any setting for viewing structure in spect list?

Re: NIST Library

Posted: Mon Jan 21, 2019 10:04 pm
by James_Ball
Two statements taken from the NIST Library web page could explain it.

"When a spectrum is associated with a structure in the Spectrum Information dialog box of the Librarian tab view, the InChI Key is automatically associated with the spectrum."

"Spectra in the NIST Mass Spectral Library may have information including formula, mass (nominal, exact, or both) names and synonyms, structures, and more"

This implies that not all entries will have all the information, so there may not be a structure reference included for that analyte. It seems to be showing the structure for the Hexadecanoic Acid Methyl Ester in the entry at the bottom of your snapshot so I would guess Methyl Palmitate does not have a structure included in the database.

Re: NIST Library

Posted: Tue Jan 22, 2019 8:14 am
by M.John
Thanks James

I've figured out that structure of compound in "spect list" has different database than the "Hit list"?
But, I expect when I inject pure standard with a match factor as high as 995 (and 98% probability), the structure is shown in "spect list". Did I get it right?

Re: NIST Library

Posted: Tue Jan 22, 2019 8:22 pm
by James_Ball
M.John wrote:
Thanks James

I've figured out that structure of compound in "spect list" has different database than the "Hit list"?
But, I expect when I inject pure standard with a match factor as high as 995 (and 98% probability), the structure is shown in "spect list". Did I get it right?


I can't answer that question as I have only used the NIST library with the Agilent software.

Re: NIST Library

Posted: Mon Aug 02, 2021 6:10 pm
by ods-at-pacific
I realize this question is over three-years old; however, in case someone runs into it, I thought it was necessary to explain what is going on.

As nearly as I can tell (the original embed graphic no longer appears in the post) the inquisitor is referring to the NIST Mass Spectral Search Program. He mentions the Spec List as the upper left window and this is an appropriate description of MS Search.

The spectrum imported to the Spec List is a line of text used as the name of the spectrum and a series of m/z values and intensity pairs. This spectrum has no correction to any of the data in the Library being searched. When the search is done, the spectrum of the best match is shown in the lower right window. The lower left window is the Hit List, which is a list of the Hits order according to their Match Factor. Each entry in the Hit List is tied to a spectrum, and its metadata, in the Library being searched. Therefore, the display spectrum will have a structure along with all of that compound's metadata (MW, CAS#, Formula, NIST#, etc.).

Just because a spectrum in the Spec List is identified as a specific compound does not mean that the structure and other metadata for the compound will become automatically attached to the Spec List spectrum. The link between the imported spectrum and the Library spectrum is the Match Factor.