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21
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

 
22
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
23
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
24
MS-DIAL / Export of feature table to GNPS
Last post by lucia190 -
Hi,

I am using untargeted metabolomics and want to export the files for FBMN in GNPS, but I can't see a GNPS export option (as mentioned in tutorials). My current version is v.5.1.231120, so I am wondering if for this version there is another option I need to select. I have tried downloading other files that look very similar to a feature table, but GNPS fails to perform the analysis saying there is an error in the file.

I am fairly new to the metabolomics community, so I appreciate any ideas/help from this community!

Best,
25
MS-DIAL / Re: MS-DIAL beginner
Last post by biswapriya -
Welcome.
You would need:
 1. at least 3 QCs, and then the "clickable" options will come-or else it would not.
2. True Positives also needs a definition from an user than a software tool:
Only MS1 match is not enough to believe the hits!)!
Above with MS2 (MS/MS) against public spectral library at say >70% cosime match is higher confidence (likely publishable).
Above both with RT (if you have an internally generated LC library for your compounds of interest!) then it's of even higher confidence.
If you have IOn Mobility generated CCS values to match then it adds to the confidence.

So you got to take your call!

Thanks,
Biswa
26
MS-DIAL / Total ion current boxplots
Last post by ncrohrbaugh -
Hello,

I am a beginner to MS-Dial, which I am using for untargeted metabolomics, and I have a question about its capabilities. In my work with XCMS, I have found that comparing total ion current between defined classes or between samples is a useful way to compare groups and identify potentially problems in MS runs.

Is there a way to see this in MS-Dial? The box plots I have seen in MS-Dial seem to only compare one identified feature at a time, and do not allow for comparison of the signal from all features identified between different groups. If anyone knows how to compare different groups on a broader scale, please let me know!
27
MS-DIAL / MS_DIAL_FAMES Dictionary
Last post by Jurica -
I trying make preprocessing GC/MS data in MSDIAL. I have problem when I use FAMES dictionary, if I use ALKANE dictionary everything it's OK.
That is, it throws me an error: The aligned EIC file (alignmentResult_2024_1_19_14_18_44.EIC.aef) cannot be found. Please excute peak alignment for the use of aligned EIC viewer.

I first time using MSDIAL, and I hope someone can help me.

28
MS-DIAL / Re: MS-DIAL beginner
Last post by ilaria. -
Hello Biswa,
thanks for your reply!
About the point 2, I am trying to normalize with LOWESS or LOWESS+internal standard but the "Normalize" button is not clickable. I set QC in correspondence of the QC run in the table where you specify the type of the data. Do you know why?
Regarding point 3, with the term "validated" I meant the assignment of the true positives compounds. Thank for the suggestion to how find them in the final table!
29
Job opportunities / Experimental Officer in Metabolomics – University of Birmingham,
Last post by e.voros -
We are recruiting an Experimental Officer in Metabolomics to join our team at the University of Birmingham. Phenome Centre Birmingham (PCB) has an international reputation specialising in toxicological and biomedical metabolomics.  We have an exciting opportunity for an enthusiastic and committed chemist or biochemist who has experience in LC-MS metabolomics. This fixed-term position is ideally suited for someone who gained experience in applying high-throughput analytical methods, including advanced robotic sample preparation and state-of-the art hybrid LC-MS metabolomics assays that combine untargeted analyses with targeted measurements of metabolic biomarkers.

Closing date for applications: 13th of February 2024

If you are interested in applying for the post please find further details on the University of Birmingham’s job site.
30
MS-DIAL / Re: MS Dial v5 keeps crashing + Mass normalization
Last post by biswapriya -
Hello,

1. MS Dial (v5) is still unstable and I would not recommend using it as many things can cause it to crash. Better use stabled 4.9 versions as I see.you have started using!: )

2. In the 4.9 version, just use the "sample mass scaled to 1" and add to the "injection volume (1 uL) column" by adding different values scaled to whatever numbers they are. Should factor in as well.

Hope this helps.
Biswa