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Messages - QizhiSu

63
MS-DIAL / Re: MS-DIAL does not export MRMPROBES library correctly
Hi Hiroshi,
Just one more thing. I found the latest version MSDIAL exports all initial identification by the software itself but ignores all manual curation even though I have ticked the ref.match box.

Best,
Sukis
64
MS-DIAL / Re: MS-DIAL does not export MRMPROBES library correctly
Hi Hiroshi,
I have tested the latest version. It works fine now. But it still includes compounds that have already been denied as identified during manual curation.  Anyway, it is fine. I can manually delete them.

Thanks a lot.
Sukis
68
MS-DIAL / MS-DIAL does not export MRMPROBES library correctly
Hi,
I have a problem with exporting MRMPROBES library. I have manually curated my UPLC-QTOF-MS data and used the default parameters to export MRMPROBES library. However, the exported table looks weird and is not the same as my identified table (see attachments).

Does anybody have experience?

best,
Sukis
69
MS-DIAL / Re: Question about MRMPROBES
Many thanks, Ondrej.
Running quantification in excel means to analyze the calibration curves by MRMPROBES using the same settings, right?
Using it for pseudoMRM is a good idea!!!


best,
Sukis
70
MS-DIAL / Question about MRMPROBES
Hello everyone,
I am new to MRMPROBES and I have something unclear. As I understand, it is a program designed for targeted quantification analysis, right? I have read the tutorial but didn't find something related to quantification settings, e.g. settings of calibration curves. Or maybe it is only designed to quantify the peak height/area of each metabolite but not concentrations? if so, what is the advantage to use it for DIA data rather than MSDIAL since MSDIAL calculates peak height/area of each metabolite already and we can simply use the area table exported from MSDIAL, no?

Any opinion is appreciated! And thanks in advance.

best,
Sukis
71
MS-DIAL / Re: Some GC-MS peaks donot correctly aligned
Dear Hiroshi,

I am awfully sorry for the late reply. I just forgot about this issue.....
It is true that these two compounds have quite close RI. I just thought that MSDIAL will take into account the spectra similarity as well.
setting quant mass for each spectrum and use quant masses defined in MSP format file do the trick. So maybe it is better to set quant mass for each spectra in the *.msp file? but if i understand well, MSDIAL will take the highest peak in each spectra as the quantmass, right?
74
MS-DIAL / Re: How to predict MS/MS spectrum of a given chemical that is not present in Pubchem
Hi Rromanas Chaleckis,

Thanks a lot. I know that we can prepare a .txt file as you said. But as I understand, in this case, MS-FINDER will fragment all chemicals provided in the .txt file and score them according to their matches to the given spectrum. However, I am thinking if it is possible to fragment a given chemical requiring no given spectrum.
75
MS-DIAL / How to predict MS/MS spectrum of a given chemical that is not present in Pubchem
Dear all,
Does anybody know how to predict MS/MS spectrum of a given chemical that is not present in Pubchem by MS-FINDER?  I am working with oligomers which could be any combination of monomers, e.g. diethylene glycol (DEG), phthalic acid (PA), triethylene glycol (TEG). However,  many of them are not present in Pubchem, for example, cyclic TPA-EG-TPA-DEG. I am thinking if MS-FINDER can work like a MS/MS fragmentator that allows input of a given structure and give us the in-silico MS/MS spectrum?


Thanks in advance!
Sukis.