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91
MS-DIAL / Re: Error in grouping Br and Cl isotopes
Last post by Hiroshi Tsugawa -
Hi Lisa,

from the last week, I checked my source code, and modified them to deal with your issue.
I completely modified isotope trackers. Especially, the previous msdial did not correctly reflect the isotope estimation results from each file's result. I hope the following developmental version is fine for you. Please let me know if it's good for you or not.
https://briefcase.riken.jp/public/f9rMQA4nJYhAN3I

Thanks,

Hiroshi
93
MS-DIAL / Commercial Libraries for use with MS-DIAL
Last post by biswapriya -
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
94
MS-DIAL / MS-DIAL and MS-FINDER questions
Last post by Borja -
I would like to ask you some questions about these softwares since I’m new with them (MS-DIAL 4.24, MS-FINDER 3.20 and ABF Converter 1.3.7328.29545):
1.   When I use the ABF Converter, the .abf files obtained from the original .raw ones have not always the same size, depending on the computer I use (despite of using the same version of the software). As a result, the number of peaks showed in the MS-DIAL MS1 changes a lot (selecting the same minimum peak height in the Peak detection tab). Are MS-FINDER MS/MS and MS-DIAL MS2 exactly the same?

2.   I have noticed marked differences regarding peak intensities between MS-DIAL MS2 and MS-FINDER MS/MS spectrums. Why does this happen? Is it due to any parameter setting I need to be aware of? That’s important for me in order to visualize the fragments, because I don´t know which is the correct one (if any of them in my current settings).

3.   Why does the molecular ion match to be the base peak in the majority of times in MS-DIAL MS2?

4.   In the MS-FINDER, is it necessary to check the “Spectral datase search” box in the “Method tab” of “Analysis parameter setting” in order to activate the data sources selected in the “Data source” tab? Which databases uses when it is not checked and when it is checked?

5.   In the MS-FINDER, despite I checked the boxes of only some of the available databases present in the “Datasource” tab, when I ran the file the metadata showed additional databases that I didn’t select.

6.   Are the databases available in the http://prime.psc.riken.jp/ page different to the ones present in the “Resources” folder downloaded in the installation of the MS-FINDER?
95
MS-DIAL / Re: Few issues about MSDIAL and MSFINDER
Last post by Sukis -
Hi Hiroshi,

" a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird.

According to my understanding, the function storing lock mass data is not stored in abf. If you see such an issue, we have to ask the developers of abf converter. Please send me an example .raw file of Waters if you face on such an issue."

I recently encountered this problem again. i think i find a good example now.

I upload two screenshots here. after removing the function 3 from the raw file, the deconvoluted MS/MS is much better.

maybe I can send you my file when you have time.


96
MS-DIAL / Re: Visualize samples' abundances as pie charts on Cytoscape.
Last post by lfnothias -
Hi,
Thanks for using the feature-based molecular network method on GNPS ! Please make sure you are following recommendations in the documentation at https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-ms-dial/

Note that for MS-DIAL's metadata in GNPS molecular networks visualized with Cytoscape, the following is required:
"IMPORTANT WHEN USING A METADATA TABLE WITH MS-DIAL: "filename" in the metadata files for FBMN with MS-DIAL should not contain file extensions (ex: "sample1.mzML" must be "sample1")."

If you need more support, please use the GNPS forum and provide the GNPS job link.
https://groups.google.com/forum/#!forum/molecular_networking_bug_reports

Cheers,

Louis-Felix




97
MS-DIAL / Re: carnitine annotation
Last post by Ondrej -
Hi Hiroshi,
thank you. Could you please also add [M]+ as a pre-defined adduct type? And eventually also [M]- for compounds with permanent charge.
Ondrej
98
MS-DIAL / MSFINDER tool "MSP TO SEPARATED MSP files" not working
Last post by Andrea -
Dear all,
I need to convert the msp file (containing the representative spectra of my alignment results exported from MSDIAL) in separated msp files. I then want to import these files in MSFINDER for a batch job.
When using the MSFINDER tool to do this, the program crashes before finishing the job. This does not happen if I use the "mgf to separated msp". Representative spectra exported as mgf lose most of the important feature's metadata though, therefore I'd rather export my representative spectra in msp.
Does anyone know how to solve this problem? Alternatively, do you know another way to separate the msp file?

Thanks a lot in advance for your help,
Andrea