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11
HMDB / How to create a csv HMDB database without programming
Last post by !ndium -
This post contains instructions for how to create a HMDB Metabolites CSV database for searching mass spectrometry spectra without using scripts such as Python or R scripts. Two options will be described with Option 1 not requiring any specialized software and the simplest approach. Options 2 uses freeware and is useful to convert sdf files. Some biofluid specific HMDB databases only appear to be available as sdf files so Options 2 may come in useful.

Option 1.
  • Navigate to the HMDB.ca website and from the top menu select “Metabolites” from the Browse dropdown
  • Choose your filters, apply the filter then select the Export button which should be below the filters on the right side (the entire database is approx 248K entries)
  • The export may take a few minutes. Try again if it does not work the first time. Once it completes the file will either automatically be downloaded to your browsers default download location or a Save As box will pop up depending on how you have things configured. Notice that the file does not have an extension. Rename the file as desired and add the .CSV extension on the end.
  • Open the file in Excel.
  • Modify as needed. For example, delete any columns you don't want, and change column headers so they recognizable by your mass spec software. For example, the Agilent MassHunter Qualitative software recognizes the following column headers:

    Formula
    Retention Time, RT
    Mass
    Compound Name, Compound, Cpd, Name
    Description, Notes, Comments
    CasId, CAS
    KeggId, KEGG
    HmpId, HMP
    Structure

Option 2.
  • Download the freeware Datawarrior from: https://openmolecules.org/datawarrior/download.html
  • Load the sdf file. Delete any columns, then go to File > Save Special > Textfile…
    Alternatives to deleting the columns in Datawarrior is to import the file from within Excel by navigating to Data > From Text and selecting the desired columns using the Excel import wizard. Alternatively you can just edit the file directly in Excel. If an error is returned when searching the csv file, considered running the Excel CLEAN function on some of the columns.


Other biofluid specific databases available through the https://www.tmicwishartnode.ca/databases/ website are offered as sdf files and, since they are subsets of the main HMDB database, are much smaller. The same biofluid databases are offered through the HMDB.ca website but only as zipped XML files.
12
MS-DIAL / Re: MSDIAL 5.1 crashing with timsTOF data
Last post by triston.groff -
I don't have a solution to this problem, but commenting to say that this has been my experience too using timsTOF Flex. Weirdly, MSDIAL version 4 works but version 5 doesn't.

I think that with MSDIAL 5, they stopped recommending converting to .ibf format because supposedly raw .d files are readable, but this has not been my experience.

Maybe this should be an issue that is opened on the MSDIAL GitHub issues page. I believe this is where they now would like issues to be posted.

Take care,
Triston
13
MS-DIAL / MSDIAL 5.1 crashing with timsTOF data
Last post by mecolley -
Hello,

I have downloaded the latest 3 versions of MSDIAL and all of them crash when I try to analyze data from my timsTOF Pro2 and our timsTOF FleX instruments. The data was collected with PASEF and I have converted the files with the IBFConverter. The data opens and is analyzed well in MSDIAL version 4.90, but I cannot get the same IBF files to process in the newer versions.

Any updates on timsTOF data compatibility with MSDIAL 5.x? Does anyone have any advice?

Thank you,
Maddie
14
MS-DIAL / Gangliosides in the Lipidomic Library
Last post by mecolley -
Hello all,

I noticed that the website was updated to list the nomenclature of the larger gangliosides ( http://prime.psc.riken.jp/compms/msdial/lipidnomenclature.html ). I am particularly interested in the GD1a/b series and am currently annotating them by hand.

I downloaded the newest available versions and noticed that in the lipidomics library (positive and negative), gangliosides above GM3 are not available.

Any updates on when they will be included?

Best,
Maddie
15
MS-DIAL / Alignment between MS1 and MS2 files
Last post by lpd_mem -
Hi everyone,
I have recently started to use MS-Dial on untargeted LC-MS/MS. I come to appreciate that it is a powerful and flexible system. And the tutorials that were put together by the developer and people in this community has been immensely helpful.

My questions is on alignment. In my study, MS1 data was acquired from all samples, and MS2 was only acquired on pooled QC samples to boost sensitivity. It doesn't seem that MS-Dial can align between MS1 and MS2 files, so as a result all the aligned peaks are missing MS2 identification. I'm curious if there is a way to align MS1 and MS2 files on MS-Dial. I would love to hear your thoughts if any of you have experience with similar issue.

Thank you!
16
MS-DIAL / How to adjust minimum peak height during data processing in MS-DIAL v. 4.80
Last post by behnera -
Hello everyone,
I have general but very important and basic question. I would like to ask you how you setting up "minimum peak height" parameter in peak detection settings before data processing in MS-DIAL v.4.8? How you setting up the treshold? Do you respect blank sample intensity? I worry about integration some noise artefacts, but don't want to lost some low intensity diagnostic metabolites. I do untargeted metabolomics fingeprinting methods with LC/-MS. My blank intensity is 6.0e6 and data were measured on tTOF Sciex 6600 system. Could you recommend which "minimum peak height" set?

Thanks a lot!
Adam
18
MS-DIAL / Potential bug reading Thermo RAW files (DDA) for versions 4.9
Last post by JeanNILU -
Hello,

I was working wit MS-DIAL v4.9 (because I like to save my spectra in txt files and export .MAT files which I can't do with versions 5+) and I had a problem with lot of spectra. The spectra are coming from LC-Orbitrap (so Thermo .RAW files) acquired in DDA with inclusion list. I imported the files without conversion and for a lot of the peaks the MS2 was missing some fragments. I am enclosing an example where you can see on top how the spectra should be (from Thermo software FreeStyle). In the middle you can see the raw and deconvoluted spectra from MS-DIAL v4.9 (missing the 78.98 fragment). And below you can see the same spectra extracted using MS-DIAL v5.1.
It looks like my problem was solved by using MS-DIAL 5.1+ so that's not a big problem for now but I just wanted to let you know that it looks like MS-DIAL v4.9 do not extract correctly the MS2 information from my files (before going to versions 5+ I tried tweaking Peak picking and MS2Dec parameters and it made no changes). The problem looks worst in negative ionization than in positive ionization for me.

Cheers
Jean

 
19
MS-DIAL / MSDIAL library format
Last post by Classic -
 I would like to know if MS-DIAL supports the usage of .TSV, .CSV, and .JSON formats for spectrum libraries.  If MS-DIAL does not directly support these formats, I would like to inquire if there is any method or tool available to convert these formats into the .msp format
20
MS-DIAL / Suspect list search (by mass)
Last post by JeanNILU -
Hi MS-DIAL users and developers,

I was wondering if it is (or could be) possible to search using a suspect list. For example, in LC can we import a list of precursor mass of interest and if some of the mass are found in your samples, the peaks would be tagged (like "reference matched" in library search)?

I would like to use a suspect list like one of these: https://www.norman-network.com/nds/SLE/ as pre-screening method.

Other licensed software allow even to import lists of molecular formula, then calculates the theorical precursor mass (depending on possible adducts) and isotopes and look for these in your samples. I can see how implementing this could be challenging but a first step could be to work with the mass only. Is this something you could see possible to add in MS-DIAL in the future?

Cheers
Jean