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Messages - biswapriya

1
MS-DIAL / Re: MS-DIAL beginner
Welcome.
You would need:
 1. at least 3 QCs, and then the "clickable" options will come-or else it would not.
2. True Positives also needs a definition from an user than a software tool:
Only MS1 match is not enough to believe the hits!)!
Above with MS2 (MS/MS) against public spectral library at say >70% cosime match is higher confidence (likely publishable).
Above both with RT (if you have an internally generated LC library for your compounds of interest!) then it's of even higher confidence.
If you have IOn Mobility generated CCS values to match then it adds to the confidence.

So you got to take your call!

Thanks,
Biswa
2
MS-DIAL / Re: MS Dial v5 keeps crashing + Mass normalization
Hello,

1. MS Dial (v5) is still unstable and I would not recommend using it as many things can cause it to crash. Better use stabled 4.9 versions as I see.you have started using!: )

2. In the 4.9 version, just use the "sample mass scaled to 1" and add to the "injection volume (1 uL) column" by adding different values scaled to whatever numbers they are. Should factor in as well.

Hope this helps.
Biswa
3
MS-DIAL / Re: MS-DIAL beginner
Hello,

1. No- cannot use Metlin unless you buy it (expensive!) and use locally- so possible if you spend USD 5K. Use MSDIAL libraries and also, you can add more LC-MS/MS libraries from MoNA (https://mona.fiehnlab.ucdavis.edu/downloads) and GNPS (https://gnps.ucsd.edu/ProteoSAFe/libraries.jsp). For combining libraries, you can use a simple method like https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-eq2ly33rqgx9/v1 but for your LC-MS/MS use case use ESI-MS or LC-MS or MS/MS libraries only. Add and combine as many as possible and does not matter Pos or Neg mode as they all help and do not mess up with matching.

2. Export "Area" or "Height" and both works fine for me. If normalized(if you ran multiple pooled QCs)  then hit normalize using LOWESS and QC or using internal standards and then export the "normalized data file" from Alignment Results.

3. Not possible. Export everything and then "filter out your validated". What is your definition of validated? If MS/MS matched with library without RT match, then fine too and can be filtered from the final area/ height file export as "MS/MS pos match" and a "cosine/ dot product" similarity score of say >70 or 0.7.

Hope this helps.

Thanks,
Biswa
5
MS-DIAL / Re: MS-DIAL error. Check polarity setting?
Hello,

Please share the a) Parameters.text file that you can save after the analysis is concluded.
b) A link to a RAW file loaded onto Google drive or dropbox will also help me troubleshoot the issue.

Thanks,
Biswa
6
MS-DIAL / Re: No support for custom .msp library in the Lipidomics workflow in MSDIAL 4.9...
Hello,
Here is a  solution that has worked for me by asking the software to run a metabolomics analysis, and uplading a lipidomics.msp spectral ibrary:

Hello,

Well, the way lipidomics workflow on MSDIAL is built is that "lipidomics spectral DB" is "inbuilt" and one can not upload external or additional libraries for spectral searches.

if you really have your own and very enriched .msp for lipids, then start as "metabolomics" in the  1st window, and then use the lipidomics .msp as reference spectral library for searching.

This should work for you!

Thanks,
Biswa
7
MS-DIAL / Re: Lipidomics MSP file can't be uploaded (lipid database setting poped up instead)
Hello,

Well, the way lipidomics workflow on MSDIAL is built is that "lipidomics spectral DB" is "inbuilt" and one can not upload external or additional libraries for spectral searches.

if you really have your own and very enriched .msp for lipids, then start as "metabolomics" in the  1st window, and then use the lipidomics .msp as reference spectral library for searching.

This should work for you!

Thanks,
Biswa
10
MS-DIAL / Re: Comparison of MS-DIAL Versions for UHPLC-MS/MS Analysis
1. 4.9 is more stable, so please use it for all LCMS/MS analyses.
2. Should show
3.In the LC world, one cannot compare RTs unless you used the same identical LC Column, buffers/ solvents, and flow rates among other LC variables that of the reported reference library/ spectra. You got to live with matching MS1 (accuracy) and MS/MS spectral matches. RT can only be indicative, for example, if a match is polar or non-polar and if the elution makes sense. If you generate your own MS/MS library in house using your own methods then RT matches can come into picture.

Alternatively check "Retip" for prediction of RT and use it as a filter OR converting RTs into RIs.

Hope this helps.
11
MS-DIAL / Re: identification doesn't work in MSDIAL
Hello,

Please share your Parameters.text file here after exporting it from your completed analysis!
I could give a look and see any obvious challenges.

Thanks,
Biswa
12
MS-DIAL / Re: Fail to detect shimadzu qgd file
Oh, wow, RushMS, thanks for that info, and did not knew that MS-DIAL i supporting so many vendor types files now!
Thanks for educating!!!! : )
13
MS-DIAL / Re: Help with Library Selection/Resources
Hi Massspek,

HMDB is NOT  a spectral library but reflects other spectral libraries. So if you want to focus on human metabolites, better to do as much annotations possible using multiple spectral libraries such as the folllowing and then sort the annotations using HMDB IDs.

1. MoNA .msp "ALL spectra":https://mona.fiehnlab.ucdavis.edu/downloads
2. GNPS .msp all spectra:https://gnps-external.ucsd.edu/gnpslibrary
3. Combine the rest from RIKEN MSDIAL server

You can combine all .msp's accessible as .text files, following instructions as here :https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-eq2ly33rqgx9/v1  when it was done for GC-EI-MS spectral libraries, but the idea is simple as once Hiroshi taught me this way!


Note: Please "ignore" using all 'w/o MS2" at all- and you are very right there.
 Also when searching against the spectral libraries you got to ignore the RT values. Only MS/MS matches at 80-90% cosine similarity fora any further analysis or interpretation !

Hope this helps.
Thanks,
Biswa
14
MS-DIAL / Re: Which libraries were the 'MSMS_Public_EXP_VS17.msp' made up of
Hi Sharon,

(1) If (2) is correct and is VERY likely- but wait till Hiroshi confirms; then (1) take precedent / priority annotation over all other libraries. Make sure your data is from negative ionization mode and if that's true given limited amount of -ve mode MS/MS spectra, this limited annotations in Public_Exp_Neg_VS17 is understandable!

Thanks,
Biswa
15
MS-DIAL / Re: Error occurred in JointAligner
Hi Roberto,
[A] Very likely that one of the files is corrupt or does not have good data. Or, one of the file is run on different ionization modes.
Just leave out a few in the set and see which is the culprit file!
At least these 2 have affected me in the past, so worth trying.....

Thanks,
Biswa