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Messages - Hiroshi Tsugawa

MS-DIAL / Re: MS2 spectrum missing peak information
Hi Larissa,

as Corey wrote, I am wondering if the two pictures showed the spectra of same precursor ion or not. (The m/z in mzmine may be the m/z of base peak, so of course, you might post the correct pictures.
I hope that the following information helps your analysis.

In fact, different software programs will assign different MS/MS information to precursor ion.
Several MS/MS spectral records will be obtained for each precursor peak from the peak left edge to right edge.
At least in MS-DIAL, an MS/MS spectrum having the highest base peak intensity is assigned to a detected peak.
And in the alignment result, one representative MS/MS spectrum will be assigned to each alignment spot by the following criteria (this is also true in GC-MS project).

(1) an MS/MS spectrum that has the highest spectral matching score among biological samples will be assigned.
Note that the peaks having 'w/o MS2: ' tag will be recognized as "unknown" in this procedure.
(2) If no annotation is existed in all biological samples, an MS/MS spectrum that has the highest base peak intensity among biological samples will be assigned.



MS-DIAL / Re: networks
Hi Stefano,

thanks, I did not realize the issue, and I fixed it today.
I will upload the new version of MS-DIAL as soon as possible, and from next version, you can export the node and edge files to be used in cytoscape.


MS-DIAL / Re: Mass Accuracy Seetings
Hi Biswa,

I would like to ask you several questions about the issue of quant mass decimals.
(1) Which msp library did you use?
(2) If you used something from my website (, note that this contains "QuantMass" field in msp.
(3) Did you use"Use quant masses defined in MSP format file" option which is available at 'identification' tab of parameter setting in MS-DIAL?

Most of quant masses that I created in the MSP files are recorded by nominal or 2 decimal values, and the decimal values will be reflected in your result for quant masses as well. Please confirm it first because I could not reproduce your result in my data set from GC HR-MS.


MS-DIAL / Re: Mass Accuracy Seetings
Thanks Biswa,

I will fixed it by the next update, and the new version of msdial (version 4.02) will be released in next week.

MS-DIAL / Re: Suggestion: Project File-Path
Hi Stefano,

well, in principle, I can create this option. But I am not sure if I could have the time to develop this utility right now...
The program will create several additional format files for saving the processed data.
(1) mtd2: managing file paths and saving parameter settings
(2) pai2: saving detected peaks information
(3) dcl: saving the EI-MS or MS/MS spectrum information assigned to each deconvoluted peak (in GC-MS) and precursor ion (in LC-MS)
(4) msp2: will be generated when you import the MSP format library in metabolomics project, and it will be generated automatically in lipidomics project
(5) arf2: saving alignment spot information
(6) aef (and related folders when the file size is big): saving aligned EICs to quickly display the multi-chromatograms when users click an aligned spot.
* abf file just has the raw spectral information only, and no processed information is attached to abf file.

These additional files are necessary to save an MS-DIAL project. But these additional files can temporally be separated from abf files if you do not want to overwrite the data by the other parameter settings.
After these additional files are moved to the folder containing abf files again, the project can be restarted safely.
Just for your information.


MS-DIAL / Re: retention index (dictionary)
Hi Stefano,

there is the auto fill option in the RI dictionary path setting window.
Please "right-click" on a data-grid cell of RI-file setting window after one dictionary file is set from the file browser, and then, you will find the option of "auto fill" there.