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Messages - Hiroshi Tsugawa

MS-DIAL / Re: Retention Time in text files - Missing peak start and missing peak end
Hi Tony,

please do
1. Export -> Peak list result
2. Choose "txt" for export format
3. Choose "centroid" or "deconvoluted" for spectra type
4. Set your directory and files that you wanna export

Again, in the alignment result, MS-DIAL does not have the function to export the retention times of peak left- and right edges.
But you can check the edge's retention times for each peak of each file by the above way.

MS-DIAL / Re: new features on File Property Setting
Dear Andrea:

thanks, I will improve the utilities accordingly in future.
Y variable will be used when you use (O)PLS-R or (O)PLS-DA in the multivariate analysis of MS-DIAL.

MS-DIAL / Re: Tables
Dear Andrea:

"Annotated Compound Table"
This is actually the utility to check the duplicated annotations in the result.
Currently, "Identified" and "Annotated" mean the ones of "Ref.matched" and "Suggested", respectively. (sorry, I will fix the header name accordingly in the next version)
Num spots means, for example, if the number is 3, three peaks have the same InChIKey (actually, based on the first 14 characters) information in the result.

"Spot Relation Table"
Actually, each peak spot is linked to other spots by some properties (within similar retention times):
(1) same metabolite, but different adduct forms
(2) similar chromatogram peak shape
(3) the precursor ion peak is included in the MS/MS spectrum of higher'm/s peak
(4) similar metabolic profiles.
You can check the linkages by the spot relation table.

MS-DIAL / Re: Exporting Error
Dear Matthew:

Did you do something like this?

1. You processed your data with e.g. MSP file A for peak annotation, and then, created an alignment result A.
2. Then, you reprocessed your data (in the same project) with MSP file B for peak annotation, and then, created an alignment result B.
3. Then, you tried to export the alignment result of "A".

If yes, the outofrange exception is due to the difference of MSPs.
Although the MSP ID stored in the alignment result A is for MSP file A, your current project (.mtd2 file) now contains the information of MSP file B. When the file sizes of MSP file A and B are different, this kind of error will be occurred.

Does it make sense for you?

MS-DIAL / Re: Post-identification issues 2
Hi Sergey,

thanks, I also encountered the same issue recently. It was completely a bug in the alignment process although the annotation is fine in annotating peaks for each sample file.
I fixed the issue, and I uploaded a trial version of new msdial here.

Could you please try to use this? and, please let me know your update.

MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Hi Sukis,

at least, the raw data/converted abf from you was fine in my side when checking the result of deconvolution.
I also confirmed that Function 3 was excluded in abf.
Could you please check the parameter setting again?

MS-DIAL / Re: Error in grouping Br and Cl isotopes
Hi Lisa,

I forgot to answer about this. Yes, you are right. The current alignment result does not have the proper isotopic patterns.
At this moment, if you need the real isotopic information for msfinder, you have to export the peak information from each analysis file result (in peak viewer). In next year, a completely new architecture of msdial will be launched in which you can export the isotopic patterns from the alignment result data.

However, I will try to implement this in the current/old msdial code for you. Please give me one more week.


MS-DIAL / Re: Molecule Annotation

if you use mzml from Thermo, please check your spectral data carefully, i.e. centroid or profile.
You can check the spectrum type by SeeMS of ProteoWizard community.

At least, at a tips for msdial processing in lipidomics project,
1. try to process your data by centroid modes for ms1 and ms2.
2. check the solvent type, CH3COONH4 or HCOONH4 in the identification setting,

for the first thing, if the spectrum type is profile mode, the spectrum peak shape looks like "peak" in the MS1/MS2 spectrum panel. Then, please restart your project as profile modes.