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11
MS-DIAL / Re: Problems with Lipidomics mode: No peaks/zero ref matches
Last post by Tomiwa Oyedokun -
Thank you everyone for your responses. I tried all your suggestions and other advice I found online but none seemed to work. I am still trying to find solution to that particular data while continuing with other tissue samples. And I will let you know when I am able to figure it out.

Thank you all,
Tomiwa Oyedokun
12
MS-DIAL / Re: Merge MS Dial exported outputs
Last post by Ruth -
Quote from: drchrispook on
Hello Cristina,
if you load each alignment to a dataframe you can use the biggest as a reference. You can iterate over the others row-by-row and test each mz/rt pair for matches against every feature in the reference. When you obtain matches you could aggregate peak areas from both dfs in a new dataframe. This is fairly straightforward in Python.
Chris

Hi, Chris. I am wondering the standard method to merge Alignments results. First, does the mz/rt pair is exactly the same or can have some tolerance? Secondly, do we need to match 'MS1 isotopic spectrum' and 'MS/MS spectrum', both the mz and the intensity?
13
MS-DIAL / MS-DIAL v4.92 lipid ontologies are incorrect
Last post by drchrispook -
In case anyone else is relying on these for filtering their data, lysophosphatidylcholines are being classified as HexCer_NDS and phosphatdylchlines as OxTG. These are obviously incorrect. I haven't tested this in any other versions.
15
MS-DIAL / Re: Impossible to import GCMS file (Hard Ionisation) [MSDial 5.1.230222]
Last post by meise002 -
Hey all,

I have the same/similar problem that I cannot select the 'hard ionisation' for GC-MS.
I have data in from a GC-quadrupole QToF (Agilent Technologies) machine. The data was in the .D format and I converted it to .abf with the Reifycs file converter (default conversion settings).
I tried the MS-Dial version 5.1.230222 as well.

Should I have changed something in the conversion settings? Or change something in MS-Dial?

Thanks for the help!
-M

16
MS-DIAL / Questions regarding waters' Cyclic ion mobility data
Last post by Xiaodi Shi -
I was trying to use MS-Dial ver4.92 to process raw data acquired by Waters' Cyclic ion mobility coupled with Agilent GC-APCI. When I use ibfconverter, there is an error (pls see attached image).

I wondered how to address this issue, and if MS-Dial can process Waters' Cyclic ion mobility data?
17
MS-DIAL / Duplication of compounds after check "Only report top hit"
Last post by Sharon -
Hello administrator,

I have a little question.
When I checked the box "only report the top hit" under identification tab, many redundancies of metabolites were removed, but not all. Could you please suggest what could be the problem and how to solve this?
Can I manually remove duplicates by the match score? Does the "total score" in the export "alignmentResult table" mean the match score?

Thank you very much.

18
MS-DIAL / Features list containing duplicates
Last post by NthlLcrmp -
Dear MS-Dial users,

I need help to understand the feature list produced by MS-Dial.

I am processing over 200 samples analysed in GC/MS. The data has been acquired in several separate batches and unfortunately there is a RT shift of up to 3.6 seconds between the batches. I performed a processing with MS-Dial version 4.9 and the parameters in the attached text file.
By looking through the feature list from the alignment, I found features with the same RT, the same distribution profile across the samples but a different quant mass. When opening the files on AMDIS I find that there is a chromatographic peak at this retention time (hopefully!), and that the two m/z selected by MS-Dial line up perfectly with the same peak shape (see attached image).
I would say that these two features belong to the same molecule and therefore there should not be two lines in the feature list. I had two hypotheses to explain this:
(1) There is a problem during deconvolution. I tested sigma values between 0.5 and 0.8, which I understand should decrease the number of deconvolved peaks, but this had no effect. I also tried increasing the EI spectra cutoff from 10 to 100 amplitude and got even more features.
(2) There is a problem with the alignment. I tried to align according to the RI rather than the RT, as each sample has its own list of alkanes, but this also had no effect.

What parameters should I change to avoid these duplicates?
Is there a way to automatically remove these duplicates?

Side question: When I look at the "Raw vs. Purified" to see the difference between the deconvoluted spectra, it doesn't change no matter which feature I look at. Is this normal?

I look forward to your suggestions

Best,
Nathalie
19
MS-DIAL / Re: MS-DIAL crashing after setting a new project
Last post by parasitetwin -
Hello everybody!
Just registered to write that this issue can be (and has in my case been) related to the comma/dot settings in windows  :'(

What worked for me was to:
- Open Control Panel in windows
- Go to "Clock and Region"
- Under "Region" click "Change date, time, or numbers format"
- Click "Additional settings"
- Change from comma to dot under "Decimal Symbol"

Hope this helps someone!