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1
MS-DIAL / Re: MS2 spectrum missing peak information
Last post by CoreyG -
Hi Larissa,

I haven't used MS-DIAL or mzmine2 enough to give you definite answers about the software.
However, I do see that the precursor masses are different between the two images. Not by much, but enough to suggest that they aren't showing the same DDA product scans. I assume this is why they differ i.e. they are showing different scans at different retention times -> different abundances of coeluting peaks.

If the software is showing the 'best product ion scans' that match a library, the difference would be in how they have implemented spectral similarity. There are many parameters that can be tuned and I guess the authors have settled on slightly different ones.

I hope that helps.
Cheers,
Corey

4
MS-DIAL / Export alignment results to .MSP file with retention time, S/N, etc. information
Last post by Sukis -
Dear Hiroshi and MS-DIAL developers,

Thank you very much for your great effort in developing and maintaining MS-DIAL. I am thinking if it is possible to export alignment results (representative spectra) to MSP files together with metadata, e.g. retention time, S/N, etc. MS-DIAL has a very good option to search against MS libraries though, it is a little bit tricky when searching against NIST as well as Wiley libraries because they don't have RI information suitable for MS-DIAL. After identified by MS-DIAL, I still have to check each identification using RI information. For me, it is more convenient to use the NIST MS Search. However,  the .MSP file exported from MS-DIAL does not contain metadata, retention time, S/N, etc., and it is a little bit tricky to correspond MSP entry to the peak spot. Is it possible to incorporate metadata, especially retention time, when exporting the alignment results (representative spectra) into .MSP file?

Kind regards,
Qizhi Su
5
MS-DIAL / MS2 spectrum missing peak information
Last post by lbarelli -
Dear MS-DIAL developers,

I have been working with both MS-DIAL and MZmine2 for analysis of a DDA dataset (ESI-LC-MS-MS with Q Exactive) as I have run into some confusion regarding the MS2 peak information. In the figures attached, you can see the MS2 of the same compound as displayed by both programs, however, there are many peaks absent in the MS-DIAL image and those shown are not the most abundant as seen in the MZmine2 image.  Is there possibly a setting that I have overlooked or incorrectly applied that would eliminate/obscure these peaks? Or is it possible that there is an issue during conversion of the .raw to .abf that may have happened? I have this issue for all my MS2 spectra of interest.

Thank you for any help you can offer,

Larissa

6
MS-DIAL / Re: Suggestion: Project File-Path
Last post by Hiroshi Tsugawa -
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.

Hiroshi

7
MS-DIAL / Re: retention index (dictionary)
Last post by Hiroshi Tsugawa -
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.

Hiroshi
8
MS-DIAL / retention index (dictionary)
Last post by spapaz -
Dear Hiroshi and MS-DIAL developers,

for GC-MS processing using RI, would it be possible to change so that the user has to define only once the reference ABF alkane file (and the txt dictionary) instead of doing it for every single ABF sample? Alternatively, if it is possible to have a "fill-down" function, or to copy and then past the path through all the sample rows at once.

Thank you!

Stefano
9
MS-DIAL / Suggestion: Project File-Path
Last post by spapaz -
Dear Hiroshi and MS-DIAL developers,

would it be possible to add a feature that would enable to:

- first step, create a Project by specifying a directory (without ABF files), where the .mtd project and results will be created and saved 
- second step, define the path to import all the ABF files from other directories (within or outside the previous project folder)

In this way the user could, 1) keep in separate locations and/or sub-folders the ABF files,
and 2) keep separate all the outcomes (alignment, etc).

If this is already possible I apologize, but at the moment I can only different the "analysis file path" from within (or, basically only the exact same)  project file folder which contains the ABF files

Thank you for this great software

Best regards,

Stefano