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1
MS-DIAL / Re: Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Last post by FalcoB -
Hi Triston,

thanks for sharing the workflow.
You mentioned "deconvolution of spectra". I suppose you analyzed your samples by DIA, right? We are using instead DDA. We are choosing one vial per compound. For each vial we have five injections by applying five different collision energies.

Is the workflow you mentioned only applicable for DDA, too?

When I look at the intensities of my fragments MS2 spectra I regularily observe the same low value for several fragments, i.e. pure noise. From my opinion, it would be nice, to have the ability to set a cut-off with respect to absolute intensity in MS2 Dial during data processing.

Best regards
FalcoB
2
MS-DIAL / Re: Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Last post by triston.groff -
Using CorrDec will help. I recommend reading the tutorial for creating an AMRT library. This was very helpful to me. CorrDec requires multiple injections at different intensities to deconvolute spectra. The tutorial says to do a 7 point serial dilution with 1 compound/vial, but this was too costly for us, so instead we did 10 non-isobaric compounds per vial and did injection series with increasing injection volume.

Good luck!

-Triston
3
MS-DIAL / Re: Possible to export MSDIAL alignment results from console app?
Last post by triston.groff -
I have been trying to figure this out for so long!!! This would be VERY helpful. As far as I can tell, all uses of the console application require GUI application as well. For many situations, it would be nice to be able to get results without opening the GUI. Exporting results tables would allow for a full analysis with the console application, but it would also be nice to be able to perform ion amalgamation, RT correction, and other MS-DIAL functions from the command line.
4
MS-DIAL / Options for Noise Cleaning of MS2 spectra for Build an Inhouse Spectral Library?
Last post by FalcoB -
Hi,

we are going to built an MSMS-library in MS-Dial (MSP-file containing MSMS spectra of reference compounds analyzed on our MS device).

Is there a possibilty to do a noise cleanup of acquired MS2 spectra during data processing? Here, I only found one parameter "Relative Abundance Cut-Off" (Identification Reiter). From my point of view this parameter only determines the way the spectral matching is done but this is not a cleaning of MS2 spectra itself. So, the only way would be to curate each single MS2 spectrum manually?

Thanks for your support.

Regards Falco
5
MS-DIAL / Crashing msdial
Last post by aziz80 -
Hi colleagues ,
 I have a problem with ms dial, I have a new computer with windows 10, when I put next in a new project the application crash and shows me this error message you find it in pj, I hope you find me a solution
7
MS-DIAL / How to self-built database for MS-DIAL
Last post by Wangtiancai -
Hello administrator, I am a new user of MSDIAL, and I want to know how to built database for analyse in MS-DIAL? At present, I know that our database should be in MSP format, but how to generate files in MSP format? And what information is needed? How should the information be arranged? I did not find the corresponding template file. By now,the information I have in hand is the MOL structure file and SMILES of compounds. Is this information enough to build a database for analysis? I am looking forward to your reply and help, thank you!!!
8
MS-DIAL / Possible to export MSDIAL alignment results from console app?
Last post by wkumler -
Hi all,
    I'm wondering if it's possible to export MSDIAL alignment results using the console application (or other script!). I'm currently using it as a kind of semi-targeted method where I run it but then go back and modify the peak boundaries for those features I know are problematic and for which I need high-quality data. I'd like to then script the export of that peak list rather than needing to go through the point-and-click process of exporting the results to a text file manually, and it seems like this is something the console app could do? Specifically, I'd like to open an existing .mtd2 file, click the "Export" tab, select "Alignment result", specify the output directory, check a couple of the boxes, change the output format to text, and hit the "Export" button at the bottom. Is this possible or planned to be included in a future update? Or does the console app only do truly hands-off untargeted processes?
    -Will
9
MS-DIAL / MS-DIAL alpha version V5.06
Last post by neo_009 -
Just downloaded the alpha version5.06.  Overall the UI is beautiful with familiar GUI interface on windows version.
Few things i have noticed:
1. This version is quite sluggish in terms of peak picking. it takes considerable amount of time as compared to all the previous versions.
2. Multi-threading didnt worked. Even if i set # of threads to 5-6, it still using only 2 threads.
3. After the search, once you go in the alignment spot viewer, MS/MS matching window annotated peaks labels seems to be shifted.
4. needs more work on the Data visualization tab, the PCA and PLS-DA didnt seemed to be working.
5. Most importantly, when i exported out the aligned peaks, if one normalize the peaks using any method (either TIC or LOWESS), peak area exported out have all 0 values. somehow the normalization task is messing with the original peak areas.
6. on a normal height/area export, MS1 isotopic spectrum is completely missing.  its just give "null" values.
7. Even on the MS/MS spectrum, it seems that if you have a MS/MS match, then only the spectrum is shown, otherwise the spectrum is "null".
8. If i use a text based database with MZ and RT information, both MS1 isotopic spectrum and MS/MS spectrum have "null" values.
9. Somehow the MS-CleanR filter is not working. 

I understand this is still an alpha version, but these are the errors/problems i found. 

Thanks Hiroshi for the continued development on MS-DIAL.  Although i found that this version can handle the proteomics data as well, but i havent tried any of that yet.

Looking forward to test the beta-version (as an when it will be released).

Thanks once again for this wonderful software

Nishi





10
MS-DIAL / Crashing msdial
Last post by aziz80 -
Hi colleagues ,
 I have a problem with ms dial, I have a new computer with windows 10, when I put next in a new project the application crash and shows me this error message you find it in pj, I hope you find me a solution