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Messages - Hiroshi Tsugawa

138
MS-DIAL / Re: MS-DIAL does not export MRMPROBES library correctly
Hi Sukis,

for this issue, I cannot reproduce your issue.
For example, how do you exclude automatically annotated metabolite information in MS-DIAL?
I personally tried to do it with Control+D that converts the annotated information (library ID >= 0) into unknown (library ID < 0).
As long as I use this, the exported reference library with the option of "Use reference spectrum to make MRMPROBS library". If you untick this option, the program always exports all peaks.

Thanks,

Hiroshi
 
139
MS-DIAL / Re: MS-Finder search parameters
Do you use HMDB library for GC-MS data? Or, do you try to use HMDB library for LC-MS?
In HMDB library, there are few information for LC-MS/MS, and there is no precursor m/z field which is required for annotation in LC-MS/MS project in MS-DIAL.
I simply downloaded HMDB msp library from mona website, and opened it by notepad++. Mostly, the contents are for GC-MS as attached.
Thanks,

Hiroshi
140
MS-DIAL / Re: Normalization
Hi,

simply, I wrote the source code to let you know how the mTIC value is calculated.
Here, LibraryID should be more than 0 if a peak is annotated by MSP library.
The postidentificationlibraryID should be more than 0 if a peak is annotated by user-defined text library containing the pair of m/z and retention time. The annotated metabolite having the tag of "w/o MS2" is excluded to calculate the mTIC value.
Thanks,

Hiroshi

Code: [Select]
for (int j = 0; j < alignedSpots.Count; j++) {
           if ((alignedSpots[j].LibraryID >= 0 && !alignedSpots[j].MetaboliteName.Contains("w/o")) || alignedSpots[j].PostIdentificationLibraryID >= 0)
                        tic += alignedSpots[j].AlignedPeakPropertyBeanCollection[i].Variable;

                    }
                }

142
MS-DIAL / Re: Exporting Error
For this, the reasons should be
(1) wrong polarity setting
(2) minimum amplitude cut off (in peak detection tab) should be lowered more.
(3) an destroyed file is imported.

I hope this information helps you.
Thanks,
Hiroshi
145
MS-DIAL / Re: when linux version of MS-DIAL will be released
Hi Wen,

thanks for asking. One issue for sharing the source code for example in a git repository is the licensing manner with MS vendors. Especially, a critical source code for reading their raw data (agilent, sciex, and bruker) cannot be distributed unless you have a contract with them. Of course, we can reorganize the .net solution project without the source codes involved to the raw data retrieving. Then, I can send it to you. But one disadvantage is that you cannot retrieve our latest updates for the source codes..
(Therefore, I always put my source codes, which can be put in public space, when a paper is published. )

Please let me know if needed.
Thanks,

Hiroshi