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Topics - biswapriya

MS-DIAL / Commercial Libraries for use with MS-DIAL

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?

MS-DIAL / Project File Path

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,
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.

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,
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,
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?

Galaxy / How to implement a 'commerical' MS data processing software in Galaxy ?

I want to run a commercial mass-spectrometry software (from GC-MS, LC-MS instrument vendors) on a cluster and also integrate into our existing Galaxy server! Computational load wise the server is huge and have sufficient capabilities. We have personnel who can do it but need to suggest them/ provide instructions.

Questions are:

    How to get the commercial tool(s) integrated into Galaxy workflow?
    What do we need from the commercial software provider?
    How to automate or semi-automate the entire process, like file upload, batch processing, obtaining results so that the outputs are human readable (say a .csv outputs etc.)!
    What expertise/ softtools does one need to have access to be able to furnish this work?

Looking forward to your advice.

Thanks and regards,
Other / Editing Wikipedia Metabolomics Page

This post is related to the outreach of metabolomics. ;)

If one Googles 'metabolomics', naturally the first hit is Metabolomics@ Wikipedia:  :)

However, this is poorly narrated, organized, content are out dated, not growing/ enriched with latest discoveries/ inventions/ tools/ workflows, no attractive pictures and so on. For instance better definitions are available  than the existing : "metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind"". :'( Also, at present the information are heavily tilted to few popular tools, and scientific groups only- the vast majority are still missing. :o

Of course other platforms exist for such information, however, Wiki is Wiki, and first hit is important for out reach. Entire community efforts, MetSoc members, EMN/ ECRs should take  a lead to do so. ::)

As a MetSoc community, EMN, ECRs it is vital for us to make/ edit the page to inform public and interested researchers on the actual potential of metabolomics, which is currently lacking. We should start EDITING on a regular basis with "pictures, tools, links, references, real (updated) definitions, platforms, applications and so on. This is of importance as far as I am concerned.

Just a suggestion- such community efforts and outreach is an important avenue to be not overlooked for a sustainable future with and around Metabolomics. :))

Thanks and regards,
Biswa Misra :))
Other / .CAL File Generation using RI Runs using AMDIS

I have run the 37 FAME Mix from Supelco on a Thermo GC-MS, using Rtx5-sil column, and wish to generate/ assign the Retention Indices to the FAMES using AMDIS or so ? How is it done to generate the .CAL file (from the .netCDF/ .raw files from Thermo with me!) so that I can compare and identify all my compounds run using same conditions (full-scan mode!).

Do I have to (a) search NIST first to assign RIs to these compounds based on their known RIs from similar columns such as DB5, HP5 etc, or
(b) I have to calculate them de novo to be able to identity and assign their RI, and use these values for "other compound" identifications ?, or,
(c) should I use the Hydrocarbon RI .CAL File inbuilt in AMDIS-NIST Library to first generate the RI for these FAMES, first ? But that is not comparable, right ?

Looking forward to your kind advice,

Thanks and regards,