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Messages - JMS

MS-DIAL / Re: RT range in aligned spot EIC
Hi Matt-are you still having trouble with this? What are your identification and alignment settings with regards to retention time? Is this LCMS data?
MS-DIAL / Re: Peak integration in MS-Dial
Hi Sergei,
I see the same issue in my EICs in Table Viewer. I manually integrate, or zero peaks that represent just noise, but that may or may not be practical given the size of your data set (number of samples and number of features) obviously.

Hey, can I ask about your File IDs 14-16 and the annotations? I am struggling with how to deal with this from a workflow perspective in my data sets. Your annotations for 14 and 16 are different from 15, presumably because you had a different spectral match for 15 as compared with 14 and 16. So, do you inspect from Table Viewer and then go into the chromatogram files themselves to assess the spectral match? Or do you assume that the best hit for that alignment spot is the best hit for the feature? Maybe you have standards that you can use to verify which would make that easier (but that is not the case in my application). Or do you do Identification after Alignment? I have tried adjusting the EI Similarity scores in Alignment and in Identification, as well as other parameters (the sigma value in MS1Dec seems to be have a big impact in improving the deconvoluted spectra). I am using single quad GC-MS so that might be some of the issue...

MS-DIAL / Re: Unable to Completely Disregard Retention Information for Scoring/Identification
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.

MS-DIAL / Unable to Completely Disregard Retention Information for Scoring/Identification
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.
MS-DIAL / How to Specify Column Polarity and use Retention Index for ID
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?