We are doing nontargeted analysis by GC-MS (single quad) and because our analytes are relatively polar, we are using a polar (Innowax) GC column. We have an alkane standard chromatogram so we can calculate Kovats RI values for our peaks.
However, can we specify in MS-DIAL that we used a polar column in our analysis for the purposes of library matching? I know that many library entries may not have polar RI values. Basically, I don't want the identification to use nonpolar RI scoring to discount spectral matches on the MS side (at minimum) and would like to use the polar column RI values as a confirmation of the identity, if possible.
Any ideas?
Thanks,
Justin
Hi Justin,
I don't know of a way to do this within MS-DIAL, so I would untick the 'use retention information for scoring' box in the Identification tab of the parameter settings, and then compare the calculated retention indices with your putatively identified compound RIs manually.
If there are so many compounds that it isn't feasible or efficient to do it manually, the webchem R package has functions for searching online databases for RI information of the compounds in your dataset and allows you to specify column polarities and retention index types - meaning you could specify only polar Kovats retention indices and then quickly screen for big differences.
Cheers,
James
Hi James-
Thanks. That is what I landed on as a strategy. We have <100 features so not too onerous to do manually. I will keep the R package in mind for future projects/applications. Thanks!
Hi Justin, if you have a NIST EI library from about 2014 on then it will have an RI library in text format that contains both non-polar (5% phenyl residue) and polar (wax column) RIs for many of the compounds. You will need to export convert the spectral library to .msp format for MS-DIAL using the Lib2NIST program. I wrote a script to matched the RI values to the .msp file entries so that MS-DIAL could then use them.
Hi Chris,
Thanks. I am interested in the script if you don't mind sending it/directing me to it.
Thanks!
Justin
Hi, sorry but I can't find it. I wrote it >5 years ago, when I was doing a lot of GC-MS. That was Nist17 anyway. I think NIST20 includes RI data in mainlib now. I may be mistaken.
C
Hi Chris,
No problem-thanks.
JMS