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Topic: Reporting of (post-processing) matches in Annotation Table - Isomer issues (Read 130 times) previous topic - next topic

Reporting of (post-processing) matches in Annotation Table - Isomer issues


I have a question regarding the post-processing option in MS-Dial. What is MS-Dial doing, when you have partially (or fully) co-eluting isomers within your post processing txt file, i.e. compounds (adducts) sharing the same accurate mass and a very similar or the same retention time.
I processed my current data set in MS-Dial using our in-house-mzRT list consisting of approx. 400 compounds (txt and parameter file, see attached). As a result, and with respect to the Annotation Table I got about 40 matches. In parallel, I processed the same data set applying our R/XCMS workflow. Here, I got up to 40 additional matches when compared to MS-Dial.
At least partially, this can be explained by the fact that in MS-Dial only one (of several possible isomers) is annotated, whereas in XCMS any entry in the mzRT list is matched one by one and will finally be reported as “match” or “nomatch”.

Here some examples:
Name                                   Adduct   mz                   RT [min]      MS-Dial matching   R/XCMS matching
MRI_Quercetin-4-Glucosid   [M+H]+   465.10275   6.12              1743 (6.11)              FT2351 (6.11)
MRI_Spiraeosid                   [M+H]+   465.10275   6.13              nomatch              FT2351
MRI_Quercetin-3-glucosid   [M+H]+   465.10275   5.65              1745 (5.64)              FT2353 (5.63)
MRI_Myricitrin                   [M+H]+   465.10275   5.58              nomatch              FT2353
MRI_Quercetin-3-Galactosid   [M+H]+   465.10275   5.60              nomatch              FT2353
MRI_Quercetin-7-Glucosid   [M+H]+   465.10275   5.61              nomatch              FT2353
MRI_D-Saccharose                   [M+H]+   343.12349   1.03              1122 (1.04)              FT1429 (1.04)
MRI_beta-Gentiobiose           [M+H]+   343.12349   0.99              nomatch              FT1429
MRI_D-Cellobiose                   [M+H]+   343.12349   0.99              nomatch              FT1429
MRI_Maltose                           [M+H]+   343.12349   0.99              nomatch              FT1429
MRI_L-Lysine                           [M+H]+   147.11280   0.87              100 (0.85)              FT0131 (0.86)
MRI_N-alpha-Methylornithine[M+H]+   147.11280   0.87              nomatch              FT0131

In MS-Dial it looks like that in case there are several co-eluting isomers only one of them (probably the best match with respect to ΔRT/Δmz?) is applied to the Annotation Table and the others are “ignored”. This result was independently whether I checked “Only report top hit” in the Identification tab or not.

Is that true?

If yes, may it be useful to report the other possible matches in addition to the top hit (especially when not checking the “Only report top hit”)? So, you would be able to manually check this “isomer issues” in the Annotation Table and no possible match (isomer) can be overlooked.

Thanks for your response.