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Messages - biswapriya

1
MS-DIAL / Re: MS-DIAL 4.38, MS-FINDER 3.46, MRMPROBS 2.60 released
Dear Hiroshi San,


 :) Many many congratulations and thanks to you for preparing newer versions of these nice tools and updating us!
  :)  ;D  :D

Loads of kudos to you for bringing such fantastic set of tools for the entire metabolomics research community in an open-source and free manner that has EXCELLENT documentation, you fix the bugs, allow great version control,  incorporate (most of) our requests, help troubleshoot our stupidest of concerns, and work hard to respond to all our queries here:))  8)  :-[


Just wanted to acknowledge your efforts and contribution to the field!!!   ;)  ;)  ;)

Thanks a lot,
Biswa  ;)
2
MS-DIAL / Commercial Libraries for use with MS-DIAL
Hello,

The question is if one can use the (a) Wiley EI-MS (bundled with NIST EI) and (b) METLIN ESI-MS (Wiley) library for use in MS-DIAL?
Have there been any success from his user community?

I am aware that at least NIST did not have formats amenable to it, but is METLIN (and NIST MS/MS) usable?

Thanks,
Biswa
3
MS-DIAL / Re: Project File Path
Thanks a lot " Sergey Girel" and "Sukis" for the advice and will take it from here and see how it goes with  me!: )
4
MS-DIAL / Project File Path
Hello,

I have a question if the "Project file path" (for in put raw file data and where MS-DIAL will generate the intermediate) files can be (a) Google Drive or (b) a Cloud service such as AWS?

Thanks for advice,
Biswa
5
MS-DIAL / MS/MS Spectra in mzML File
Hi Hiroshi,

I am trying out a single +ve mode LC-MS/MS DDA data file (CE: 40 eV) acquired data for MS-DIAL processing.
Though, upon conversion to mzML using msConvert (oth 32 , 64 bit did not work out, peak picking all conditions did not help) can see lots of MS2 spectral data using Mass++ (See pic below) but can not see any MS/MS spectra in MS-DIAL interface (see pic). Attached are the parameters (.txt file) used too. Why is MS-DIAL not able to find the MS/MS data in my processing workflow ?

Not sure what am I doing wrong in MS-DIAL for this single data file ?

Thanks a lot for the help.

Biswa
8
MS-DIAL / Re: Problem with converting NIST library to MS-DIAL
Hi Hiroshi, Sergei,

I too face same issues from converting entire NIST/ spectra to MS-DIAL readable MSP. (though both MSPs).

I have uploaded 5 files here (A-E, the forum does not allow uploading of .MSP as reading it as .exe so attached them as .txt file)


For “1. could you please send one .msp spectral record created by lib2nist?” see:[/b]
A-“NIST_Spectra_Export”. gif showing exporting individual spectra from NIST (glutamic acid) and it looks as
B- “Glutamic acid_From_NIST_MSP”

For “2. could you please share the detail of how you convert your nist library format file to msp file in lib2nist?” I did following

C-   Converted an openly available EPA Starter Kit  spectral library using LB2NIST program and the process “LIB2NIST_from_EPA”.gif shows it.
D-   “EPA_Library.MSP” .gif shows the library.
E-   “EPA_Starter_LB2NIST_ConvertedMSP” .text is how the spectra looks like.
Hope it helps address our concerns!

Thanks a lot for the help,
Biswa
9
MS-DIAL / MS-DIAL Wish List for 2020-2021!
Hi Hiroshi,

Thank you for all the quick answers and continually improving the greatly useful tool!! : )

A wish list to request you for further consideration (based on challenges I face and where I feel MS-DIAL could help me!) :

1. What it takes for MS-DIAL to also recognize the spectral library/DB as “.mgf” format as well? In that way in addition to .MSP we can also use, for example entire GNPS Natural Products libraries amounting to thousands of spectra being added on a daily basis for MS-DIAL annotations ? Esp. When .mgf to .msp format conversions are not trivial .

2. Integration of “MS-FLO” into MS-DIAL would help In (a) consolidation of feature redundancy issues, and (b) help one report unique features from positive and negative mode runs as well ? 

3. I see pathway functionalities  added in MS-DISL but with KEGG not ideal for lipidomics data mapping or enrichment, adding “ChemRICH” as a MS-DIAL option would be fantastic for a user! Esp. with many untargeted LCMS workflows capturing bunch of lipids, doing separate pathway analysis for metabolites and lipids do not make sense !!

4. Lastly, may be a goal for 2022, I would like to see support for GC xGC (2D GCMS) data (.cdf) data analysis given the current LACK of open source tools in this area and monopoly of 1-2 vendors (and matlab tools) leading to inconveniences !

Looking forward to your thoughts and some promises!

Hope we all come out of this COVID pandemic unscathed! Stay safe and healthy!!!!

Best regards,
Biswa
11
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
12
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

13
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
14
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
15
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