Hi Hiroshi,
I was wondering why in some deconvoluted features the QuantMass is not the major mass observed in the representative spectra, like in this case (attached). Is there a setting to change this?
Thanks
Stefano
Option-->alignment result property setting, then you can input what you like!
In my opinion, QuantMass does not necessarily be the major mass. I think the most abundant unique mass is the ideal QuantMass.
Hi,
Thanks. Yes I am aware that one can change each one of the QuantMass manually in the alignment result. I was wondering if there is a way to define how the QuantMass is picked. I assume(d) that it is the most abundant mass, but that does not seem to be always the case.
Hi, I have actually realized this issue recently. The problem is that the algorithms to retrieve (A) the representative spectrum from samples and (B) the quant mass from samples are different and independently performed. Therefore, I should modify the program to (for example) retrieve the quant mass candidate from the masses included in the representative spectrum.
I will fix the program till the next update.
Hiroshi
Thank you Hiroshi.
FYI, the spectra I posted above is from a GC-Orbitrap project.
Questions:
1) is it the same way how the algorithm work for the QuantMass, between a GC and an LC project?
2) how does the algorithm decide for the QuantMass, between preferences for the most abundant ion and higher m/z values?
Thanks
Stefano
Hi Stefano,
as we discussed privately, I will write the summary of how to select quant mass in GC-MS project and of the future plan.
And actually, please see the detail in MS-DIAL version 2 paper on Nature Methods 2018.
https://www.nature.com/articles/nmeth.4512
1. First of all, the chromatogram deconvolution is performed by the information of "pure" extracted ion chromatogram of several m/z values.
2. The quant mass is determined from such m/z values producing the singlet/no-coeluted chromatographic peak.
At least in TMS-based GC-MS based metabolomics, m/z 147 (2xTMS moiety) becomes base peak in EI-MS spectrum for many metabolite features, and therefore, such the m/z value should not be used as the quant mass even though the m/z value is the base peak's m/z value.
Of course, the quant mass values can be changed by the quant mass manager of MS-DIAL.
In the next update of msdial, I will prepare the option where the quant mass always becomes the base peak's m/z value, which should be useful in GC-MS metabolomics not using TMS derivatization.
Thanks,
Hiroshi
Hi Hiroshi,
" In the next update of msdial, I will prepare the option where the quant mass always becomes the base peak's m/z value, which should be useful in GC-MS metabolomics not using TMS derivatization "
Thank you! That will be very valuable for us not using derivatization!
Best
Stefano
Hi Hiroshi,
How do you make sure that the quant mass picked by MS-DIAL for a particular metabolite is always the same in a large data generated in several batches? Is this possible for TMS derivatized samples analyzed in a high resolution GCMS?
Does the changes in quant masses of same metabolite in different batches analyzed by MS-DIAL affect the base peak areas intensities used for quantifications?
Thanks
Isaac
Dear Isaac,
For the data comparison in the large scaled data set, we should keep the same quant mass value for metabolite quantification.
MS-DIAL offers such an environment.
(1) if you put "QUANTMASS: " field in your msp format file, the metabolite is always quantified by the target m/z.
(2) Go to "Quantmass browser" of "Post processing" in the msdial menu, then, you can define the m/z values for each metabolite.
The first option should be used if many biological samples are sequentially analyzed for a long time.
Hiroshi