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 ?!!!? ; )
... 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'. ...  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.
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! : )
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!
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. : )
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!!!
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!)
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! : )
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?
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?
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?