Unable to Completely Disregard Retention Information for Scoring/Identification

July 20, 2023, 06:21:18 PM

We are analyzing samples by GC-MS, single quad, EI. We are using a polar (Innowax) column for separation as many of the analytes are relatively polar. We have alkane retention data from an alkane standard so we are using RI or RT=Use retention index(RI) and Index Type = Alkanes (see "Alignment.png")

Because non-polar GC columns (e.g., DB-5) are the most commonly used and the database RI values are based on these columns, we have turned OFF the "Use retention information for scoring" in the "Identification tab".

However, even though we have "unchecked" use retention information for scoring, it seems that MS-DIAL is still preferentially matching the unknown spectra to a library entry based on the retention index value (which is incorrect since the library entry and our experimental data were generated on a different column phase).

You can see this in the images below-in "Compound Search.png", the top compound in the Library Search ranking is Benzoic Acid, but the identified compound is Benzoic Acid, N'(6-chloro-3-cyano-4-methyl-2-pyridinyl)-N'-methylhydrazine, which is a much poorer spectral match (Compound Search 2.png). The difference is that the RI values agree better for the Benzoic Acid, N'(6-chloro-3-cyano-4-methyl-2-pyridinyl)-N'-methylhydrazine.

Is there another "disregard retention information" box that I am missing?
I think I found a work around, by initially loading the RI file but then selecting to use RT instead of RI in identification. This calculates the RI for us but identifies 0 compounds-I guess I was hoping that we could have MS-DIAL do at least the initial identification.

Re: Unable to Completely Disregard Retention Information for Scoring/Identification

Reply #1 – July 22, 2023, 04:22:34 AM

For pure spectral matching to your NIST23 library (jealous!), in your identification settings tab just set the RT and RI tolerances to 10,000. It will stop penalising matches by RT delta.

I don't know about NIST23 but if you want RT matching you need to make sure that the RI values for the NIST library are from their polar column values. In NIST 2020 there's a file in the nist_ri folder called ri.dat, which you can parse to a plain text file with both nonpolar (5% phenyl) and polar (wax/PEG) column data. You'll need someone to write a script to combine the data with your .msp export.

Re: Unable to Completely Disregard Retention Information for Scoring/Identification

Reply #2 – July 26, 2023, 01:29:14 PM

Hi Chris,
Thanks for this-indeed, widening the RI and RT tolerances gives a match based completely on spectral match. Thank you!

The downside is that this makes the processing quite slow. For 15 samples, GC-MS single quad, it's about 3 hours. Not sure if you saw a similar issue when you have used this work around?

I will look into the script writing and incorporating the polar RIs.

Justin