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Topic: MS-DIAL Wish List for 2020-2021!  (Read 454 times) previous topic - next topic

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
Biswapriya B. Misra, PhD
Assistant Professor
Center for Precision Medicine
Department of Internal Medicine
Section on Molecular Medicine
Wake Forest University School of Medicine
Cell: +1-352-215-6040
Office: +1-336-713-4622
Profile: http://profiles.wakehealth.edu/display/Person/bmisra

Re: MS-DIAL Wish List for 2020-2021!

Reply #1
Thanks Biswa! I will keep them in mind.:D
Hiroshi

Re: MS-DIAL Wish List for 2020-2021!

Reply #2
Hi Tsugawa-sensei,
I echo Biswa's sentiment and am very thankful for the continual development of tools! As additional points:

MS-DIAL
1. Is it possible to add the option to sepcify only using forward or reverse spectral matching?
2. Is it possible to add a paired mass difference (reactomics) networking function for LC-MS1 data?
3. Is it possible to enable LC-MS1 searching into MS/MS spectra I.e. via an in-source fragmentation algorithm?

MS-FINDER
4. Would it be possible to include RI for exported GC data, especially to be included in exported MSP/ MAT files.

MRMPROBS
5. Is it possible to add the capability of using mzML for SCAN data? I also assume this wouldn't need function ID as per MRM.

MS-LIMA - (thanks to Tada-san for this excellent addition)
6 Is it possible to add the ability to export a list of most abundant (e.g. top 5) ions from a spectra in the MZmine list format? This would also greatly help with integrating GC data into MRMPROBS. 
7. For GC data, is it possible to calculate or include a substructure similarity search e.g. via MACCS fingerprints?

Thank you again for all the efforts.
Best,
Elliott

P.S. The updated CompMS website design is great.



Re: MS-DIAL Wish List for 2020-2021!

Reply #3
Hi Hiroshi,
I was reviewing the latest public MSPs (MSMS-Public-Pos-VS14.msp) to understand the “Ontology” meta- information. I wanted to sort the results into compound classes based on the Ontology parameter, but I was not very successful.

Do you think that it would be possible to unify the Ontology classes according to MeSH classification?
Dinesh Barupal did this (http://chemrich.fiehnlab.ucdavis.edu/) and I think that curated classification would make the libraries much more useful. You already have the INCHIKEYs and SMILEs in the file. Some SMILEs and INCHIKEYs are not the "correct" ones that are registered in outher datagases (PubCHem, HMDB, etc.), but I think that (at least for lipids) it could be improved and converted.

Best,
Ondrej

 

Re: MS-DIAL Wish List for 2020-2021!

Reply #4
MS-DIAL

1) Normalization using peak areas
2) Semi-quantitation using again peak areas if internal standard and calibration measurements are present. Or, at least, approximation from internal standard if concentration is known.

MS-FINDER

1) I'll join to ElliottJP's post above - MS/MS fragment search in is-CID spectra.

GENERAL

1) To add some error messages upon crashes - to get at least a clue what caused the problem. Like in case with different separator settings in system  locale.