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1
MS-DIAL / Suggestion for "New Project" --> simplify creation of Sample List
Last post by spapaz -
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
2
Vendor specific software / QC correction in Compound Discoverer (ThermoFisher)
Last post by djb17 -
Hello,

ThermoFisher's compound discoverer provides two different methods of correcting for drift using either linear or cubic spline regression.

I'm not too well versed in statistics and was wondering if someone could help me understand how this is done (especially cubic spline).

For example, what would be my coefficients (beta's) if I was using linear regression to correct for drift?

Thank you.
4
MS-DIAL / Re: Problem with converting NIST library to MS-DIAL
Last post by Hiroshi Tsugawa -
Hi Biswa,

thanks. I understood. I also encountered the same issue previously.
Which version of lib2nist do you use right now?

It's because the lib2nist you used is an older version for converting nist msms query to the msp format file.
The file you shared is not the msp format file for MS/MS defined by the nist document.

Please download the latest version of lib2nist.
My version is actually

-------
May 01, 2017.

This beta-release of Lib2NIST version 1.0.6.3 mass spectral data
conversion program consists of the following files:
--------

At least it works well. And the msp format from lib2nist is something like:

Name: Desipramine
Synon: $:04267.19
Synon: $:28HCYAFALTSJYZDH-UHFFFAOYSA-N
Formula: C18H22N2
MW: 266
PrecursorMZ: 267.19
CASNO: 50475
Comment: NIST Mass Spectrometry Data Center
Num peaks: 6
196.19 52
208.11 74
208.87 2
210.29 5
222.20 13
236.19 999

by this version.

Thanks,

Hiroshi


5
MS-DIAL / Re: Problem with converting NIST library to MS-DIAL
Last post by biswapriya -
Hi Hiroshi, Sergei,

I too face same issues from converting entire NIST/ spectra to MS-DIAL readable MSP. (though both MSPs).

I have uploaded 5 files here (A-E, the forum does not allow uploading of .MSP as reading it as .exe so attached them as .txt file)


For “1. could you please send one .msp spectral record created by lib2nist?” see:[/b]
A-“NIST_Spectra_Export”. gif showing exporting individual spectra from NIST (glutamic acid) and it looks as
B- “Glutamic acid_From_NIST_MSP”

For “2. could you please share the detail of how you convert your nist library format file to msp file in lib2nist?” I did following

C-   Converted an openly available EPA Starter Kit  spectral library using LB2NIST program and the process “LIB2NIST_from_EPA”.gif shows it.
D-   “EPA_Library.MSP” .gif shows the library.
E-   “EPA_Starter_LB2NIST_ConvertedMSP” .text is how the spectra looks like.
Hope it helps address our concerns!

Thanks a lot for the help,
Biswa
6
MS-DIAL / Re: molecular networking
Last post by spapaz -
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


9
MS-DIAL / Re: molecular networking
Last post by Hiroshi Tsugawa -
Hi Stefano:

1) does the similarity cut-off represent the edge cosine score (exactly as in GNPS)?
Probably, no. At least, the concept is same, but the algorithm detail should be different from GNPS.
See the method detail in Nature Methods 2019.
https://www.nature.com/articles/s41592-019-0358-2

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?
OK, I will make it in near future.

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

Hiroshi


10
MS-DIAL / Re: Question about replicate identification
Last post by lh1989 -
Quote from: Hiroshi Tsugawa on
Hi Luann,

yes, this should be the point that I should improve in GC-MS project.
To know how the quant mass is selected, please see the below chat.
http://www.metabolomics-forum.com/index.php?topic=1412.msg4232#msg4232

In the current program, you will see such a result in GC-MS project, and if I were you, I just simply delete one of the features in the excel program.
Another option: you can tick the option of "only report top hit" in the identification tab of MS-DIAL parameter setting.
One of the duplicates or more same annotations from the same database ID is selected by considering the identification score. That is, the peak having the highest score for metabolite annotation will have the metabolite name and the others are assigned as "Unknown".

Anyway, I will improve the program as much as possible.

Hiroshi


Hello Hiroshi,
   Thank you for your reply!