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Messages - biswapriya

47
MS-DIAL / Re: GC-TOF data in MS-Dial
Hello,

Hope your Leco CDF data is not from 2D (GC x GC) runs? Then it surely runs into problems and does not handle 2D GCMS data.

Also, alternatively, using Mass++ (https://www.mspp.ninja/?lang=en_us) you can convert those .CDF (if obtained from 1 D GC-TOF instrument) files into .mzML first, which works great with MS-DIAL.

Thanks,
Biswa
48
MS-DIAL / Re: GOLM mass spectrum library with MS-DIAL
Hi Dmitry,

I feel that the GOLM MSRI library is not included in the Demo cpd library in MS-DIAL.

But, learning from Hiroshi, I have now created a document where you can add any library you wish to the demo and other libraries in .msp. The steps/ workflow is listed now at protocols.io : https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn  (see Step 5).

Hope it helps.

Thanks,
Biswa

49
MS-DIAL / Re: MS-DIAL to MoNA Spectral Submission Interface
Hi Hiroshi,

I see that the export option (spectral submission from MS-DIAL to MoNA) initiates and then runs into errors. Its not working, as I can independently log in into MoNA DB but not through MS-DIAL interface (as it does not recognize ID/ password!). Please see the same 3 screenshots too.

I hope you had a chance yet to contact with Diego, Sajjan, Gert et al ?!!!?  ; )

Thanks again,
Biswa
50
MS-DIAL / Re: Questions about lipidomics database setup
Hi Zhang,

I can try to answer the 2 questions:

[1] If you got to the MS-DIAL page: http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/ you can find information on the internal lipids DB and mentioned as follows:

...
LipidBlast fork (Last edited in December.26, 2019)
Currently, MS-DIAL internally has in silico MS/MS spectra for lipid identifications. Below is the LipidBlast (fork) templates that MS-DIAL partially uses.
Binary file (lbm2) for MS-DIAL lipidomics (adjusted Oliver Fiehn lab LC-MS method): Download
Binary file (lbm2) for MS-DIAL lipidomics (adjusted Makoto Arita lab LC-MS method): Download
Binary file (lbm2) for MS-DIAL lipidomics (adjusted Kazuki Saito lab LC-MS method): Download
LipidBlast template for glycerolipids.
LipidBlast template for sphingolipids.
These libraries are also available as MSP format: Positive (32 class, 110,833 molecules, 143,342 spectra) and Negative (48 class, 154,770 molecules, 342,454 spectra).
The original LipidBlast is available from here.
The nomenclature for lipid classes in MS-DIAL lipidomics is shown at 'Lipid nomenclature in MS-DIAL lipidomics'.
...
[2] To enrich or add more .msp files/ spectrum, Hiroshi also taught this to me as to how to do it using  a .txt file; and this I have put in as a protocol.io (method)  file freely accessible and you can follow steps and successfully generate your own library (by adding these new .msps onto the existing spectral libraries/ DBs) : https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn

Let me know if this is what you were looking for!

Please correct me, Hiroshi if anything is incorrect or amiss.

Thanks again,
Biswa
51
MS-DIAL / Re: Mass Accuracy Seetings
Hi Hiroshi,

Thanks again!

As you can see in the screenshot (attached), that indeed that mass accuracy issue has been resolved for the Quant Mass for all the runs/ analysis irrespective of whether Quant Mass is specified during the analysis or not- in the new MS-DIAL version 4.1! : )

This is great!!!!

Thanks again,
Biswa
52
MS-DIAL / Re: Mass Accuracy Seetings
Hi Hiroshi,

Thanks a lot for resolving the issues on a fast track mode and promptly so!

"2. The high resolution's quant mass should always be displayed if you do not use "Use quant masses defined in MSP format file". :  This should be so useful in 'fragment matching/ prediction'  etc. which was lost in the final  results for whatever reasons! : )

I will give a try on the 'quant mass ON' and see if it's AM or not in future runs esp. when we have unique Quant Mass for each spectrum from the in house HR EI-MS library .

This is good explanation of how the function  works and so useful in understanding!

Thanks again,
Biswa
53
MS-DIAL / Re: MS-DIAL to MoNA Spectral Submission Interface
Hi Hiroshi,

Thank you for the update and the reactivation!
Yes, indeed I checked with the new MS-DIAL version 4.1 it's working and the option is activated.
Its so convenient to submit experimentally identified structures (knowns, unknowns, and now HREI-MS spectra) directly to MoNA!!

I do have an account with MoNA and see it works. : )

Thanks again,
Biswa
54
MS-DIAL / Re: MS-DIAL version 4.10 and MS-FINDER version 3.26 were released.
Hello Hiroshi,

Thank you for the updates! Really cool to have updated tools for processing, analysis and annotation!

Question: With issues such as 'version control' / 'versioning' how does one keep track of various versions and their capabilities or say, changes?

Would it be not very helpful for the user community to learn as to whats "new in this version" (i.e., ion-mobility)  or if 'anything has changed' (i.e., processing algorithm etc.) ? In that case, a short note as a .txt file/ PDF stating it explicitly with every newly released version would be helpful for all users for both the tools? I see a lot of versions over the past year (which is great!) and then the recommendation automatically becomes to use the 'latest release' ?

Looking forward to more excellent functions and newer tools in the New Year 2020 from you!! All our best wishes for a prosperous and productive new year!!!

Thanks a lot,
Biswa
55
Other / Re: Converting .dat ASC II File with EI-MS spectrum




Hi Corey,

Thanks for the help/ advice! I have no clues what's inside after unzipping 30 GB of data/ folders as given in the earlier links.

But, I believe as they are from CFM-ID predictions (for EI-MS spectra) described here http://cfmid.wishartlab.com/data and here https://sourceforge.net/p/cfm-id/code/HEAD/tree/supplementary_material/predicted_spectra/  I believe their format is as attached 2 example files); and could be joined together into these large .dat files. 

I assume they contain predicted annotated spectra (EI-MS) for all the structures and joined together? Unsure post download how would I make into .msp formats for further use (which is the next question going forward of course!)

Thanks,
Biswa
56
MS-DIAL / Re: Mass Accuracy Seetings
Hi Hiroshi,
Thanks a lot for helping with these smaller yet significant issues!: )
I understand, adding “Exact masses” one by one or by calculation, either ways are very unhelpful!

I have 2 updates for you based on the above:

(1)   Firstly, as you see the attached snapshot, keeping the “Quant masses  Defined in msp format file OFF”  did not help (and actually got worse, and lost all the previously “displaying” HR exact masses too!). And as before, the “EI spectrum” columns are all AMs.

(2)   It has a decent (lowering # of hits!) Impact on the “performance” of identification ( if you kindly remember, I am blasting HRMS spectra against a mix of HRMS spectra plus unit resolution spectra!)  as follows:

ID vs Alignment Priority   Total                    Annotated         Unknown    Noise
Use Quant Masses Defined in MSP Format File ON     437   235   184   125
Use Quant Masses Defined in MSP Format File OFF   396   185   183   101

      
(Note: Do not add the numbers above as I have different naming conventions etc., but the performance in terms of matches went low with OFF!)

As a NOTE to future/ current  MS-DIAL users, I can attest easily, that keeping any of the options OFF is resulting in less # of hits in terms of annotated IDs and match quality, i.e.,

Use RT for scoring ON
Use RT Info for Filtering ON
Only report the top hit ON
Use Quant Masses Defined in MSP Format File ON
Identification After Alignment ON

See what makes sense and please advice for (1), (2) or we have to switch to the format where we OD have Quant Mass clearly specified: which is a big task for in house spectrum (time intensive!) and other open source sources! : )

Thanks again,
Biswa
57
MS-DIAL / MS-DIAL to MoNA Spectral Submission Interface
Hi Hiroshi,

I used to see that the "MS-DIAL to MoNA" spectral transfer button was ACTIVE previously. And I could submit some "matched and known spectra (confident hits against libraries) directly to MoNA. I understand that for Unknowns this might not be helpful etc. For known and confident matches this would help enrich MoNA esp. for EI-MS (HRMS) spectra among others.

This was SO convenient! : )

Second part of the question is that, with correct meta-data (i.e., origin from serum, or plants or microbes!) even unknowns as unknown (As tags) would be so useful in future annotations.

But a  specific reason why was it removed or in the future will be active?

Please see the attached picture!

Thanks again,
Biswa
59
MS-DIAL / Re: Mass Accuracy Seetings
Hi Hiroshi,

Thanks for the responses!
(1)   Your public libraries (all pooled from RIKEN, MoNA: all EIs) + my in house HR Orbitrap Libraries, of course, all pooled.
(2)   Yes, all from your RIKEN website, plus in house libraries. I see that the exact masses (see attached picture of 2 examples from EI-B and Fiehn-EI spectra) that in deed the masses are nominal mass, and the Exact Mass is several decimal places.
(3)   Yes, I used the “use quant masses defined in the MSP format file”. So question now is: If I uncheck this (= cross/NO), the Quant Masses column will be empty or will be those form the Query (and as I use HRMS spectra, this would be fine!)?

No wonder, I got a mix of nominal and accurate mass lists in the results.

I understand the nominal masses/ 2 decimal values for pre-existing libraries of the past or those available as open source.
I guess I now understand the issue, and unchecking the ‘quant mass defined in the MSP format file” is my solution?

Thanks a lot,
Biswa
60
MS-DIAL / Mass Accuracy Seetings
Hello MS-DIAL Developers,

In the MS-DIAL Results (output files), I see that the 'Quant mass' column does not have 5 decimal places (mostly 2 decimals and rarely 2, random?) covered for the  HRGC-EI-MS data, though the 'EI-spectrum column' covers all 5 decimal places. And I checked its not hit/ library specific and very random.

Please see the attached snapshot.

Is there a setting while exporting results to specify for consistency?

Thanks,
Biswa