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Messages - spapaz

17
MS-DIAL / normalization
Hi Hiroshi,

Question about normalization (performed with LOESS + IS).
In my Alignment results I have a total of 3300 features. When I export the results of normalization (performed with LOESS + IS),  however, in the pdf report I only see 365 features (one feature per page). 

- Why not all 3300 features are reported in the pdf? Are the features missing also normalized like the rest?

The exported Normalized txt table instead contains all 3300. Comparing values of features (found in the pdf report and not) between the Height and the Normalized txt tables, I would say all features have been normalized.

In addition, could you consider for future versions:

-In the pdf report, would be possible to order the features by their ID number?
-Would it be possible to normalize also the area (not only the peak height)?

Thank you!

Stefano


 
18
MS-DIAL / Re: Suggestion for "New Project" --> simplify creation of Sample List
Quote from: romanas chaleckis – on
you can simply copy paste all the sample details (including sample type) from an excel spreadsheet  ;)

Alright, I tried now to copy and paste from Excel and indeed it works even for the "File Type" column (drop-down menu). Thanks! This is going to save a lot of time. Maybe you can add it as pop-up tip in that view to help other users in the future! :)
 
20
MS-DIAL / Suggestion for "New Project" --> simplify creation of Sample List
Hi Hiroshi,

when creating a new project, in the "New Project Window", would it be possible to make it easier to define the type of samples?
i.e. the Class IDs and especially sample Type (currently scroll down menu, with options Sample, Standard, QC, Blank)
It is very tedious to have to set manually one by one, when we have hundred of samples. 

I would imagine two better options:
1) a "Fill down" option (similar to the one available for setting the alkane series dictionary path)
2) even better, the option to import the sample list from a user defined CSV file (strictly following the MS-DIAL format requirements)

If similar short-cuts are already available and I am missing them, please let me know :)
I did not find them in the pop-up tips, nor mentioned here: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-2-2

Thank you again for your work and incredible support!

Stefano
21
MS-DIAL / Re: molecular networking
Hi Hiroshi,

Thanks for considering all these suggestions.

About:
3) could you add more explanations relevant to these settings and different cut-offs (in their respective fields, as "pop-up" tips in the menu, but also if possible in the MS-DIAL tutorial page)?
Is this not enough yet?
https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial#section-6-3

I am familiar with GNPS and FBMN, still I am not completely sure if I interpret correctly (and how to adjust accordingly) these 3 different parameters:

1) - Relative abundance cut off [%]. e.g. 1  --> is this the threshold for the ion intensity, i.e. the higher the set value the fewer the spectra kept into consideration in building the network? What would you suggest as a default value?
 
2) - Similarity cut off [%] --> this is clear (i.e. similar to the cosine score in GNPS)

Check-box (Ticked) -Export ion abundance correlation among samples
3) - Similarity cut off [%] --> does this refer only to the "check-box" above, for exporting ion abundances correlations?

I think some  "pop-up" tips like your nicely put for other data-processing fields it would help also other users who perhaps never run a molecular networking before.

Thank you once again!

Stefano


23
MS-DIAL / Re: question about QuantMass
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
24
MS-DIAL / molecular networking
Hello Hiroshi,

I have some questions regarding the generation of molecular networks within MS-DIAL, as -->Export --> Molecular spectrum networking export:

1) does the similarity cut-off represent the edge cosine score (exactly as in GNPS)?
2) is it possible to set a minimum of matched peaks in the spectra? e.g. 4-5 peaks, and exclude consensus spectra with less than a threshold?
3) could you add more explanations relevant to these settings and different cut-offs (in their respective fields, as "pop-up" tips in the menu, but also if possible in the MS-DIAL tutorial page)?

Thank you so much

Stefano
25
MS-DIAL / Re: crash MS-DIAL --> MRMPROBS
Hi Hiroshi,
Thanks for fixing this, it seems it is not crashing anymore. But I am still experiencing some little problems with this. I am using MS-DIAL v 4.18, anf GC-MS data.

First, I tried to change one of the unknown aligned peaks to the metabolite name (my internal standard) and I would like to export only that peak to MRMPROBS. During the process it happens this:

1) if I don´t tick "export the focus (target) peak spot", then MS-DIAL exports all the features (unknown labels)
2)  if I tick "export the focus (target) peak spot", MS-DIAL exports the correct feature, but the unknown number (e.g. 218) is not from the alignment results, but from a single sample focus spot (e.g. 228). Also, it is not reporting the metabolite name, that would be useful too.
3) if I instead right click on the aligned spot, and I select "copy as MRMPROBS reference format", I only get the metabolite name (the one I wrote), but nothing else

If possible, it would be great to be able to export the aligned spots!

Thanks a lot!

Stefano
 
27
MS-DIAL / Re: Delete features
And, the other way round. Would it be possible to have the functionality to "add" a new feature
E.g. similarly as from the table chromatogram viewer for manual curation?
28
MS-DIAL / Delete features
Hi Hiroshi,

would it be possible with the next version, to add the possibility to delete a feature directly from the Alignment Table (e.g. right click--> delete) ? That would be great while doing manual inspection of the features

Thanks!

Stefano
29
MS-DIAL / Re: Manual curation of Alignment
OK great, thanks.
I assumed that, but in other software I worked with the aligned peaks are always shown like in panel 2, so it was not super intuitive :)
30
MS-DIAL / Manual curation of Alignment
Hi Hiroshi,

I am not sure if I do this steps correctly. I am following the instructions.
The second middle panel looks good with the peaks aligned, but the third panel  -"manually curated chomatograms"  - does not Update, and looks exactly the same as the top panel before manual curation.  See attachment

I see that in the bottom panel, it changes the color of the integrated chromatogram area.  Is it correct that the position of the chromatogram in this panel remains as in the first top panel (and not as in the middle one) ?

Thanks

Stefano