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Messages - agentfourtea7

1
MS-DIAL / Re: MS-DIAL file import: sorting
Quote from: biswapriya – on
Hi,

If you go to Option - > File Property Setting and then just try to click on the table and sort it works for sorting for all of them: Batches, Analytical order and so on.

Yes, you can type and make them alphabets or numbers or hybrid ones such as 1, 2, 3, or A, B, C or 1A, 1B, 1C and so on!
Worked for me just now.

Thanks,
Biswa



Thank you Biswapriya, I have tried the same now and it works. Great job!
2
MS-DIAL / MS-DIAL file import: sorting
Hi,

Has anyone else faced the odd issue where MS-DIAL does not allow you to change file name/order after import? It imports in a weird alphabetical order and you cannot change it. So if my file names are 1 - 150, MS-DIAL imports them in this order:

1
10
11
12
13
14
15
.....
2
20
21
22
23
24...

and so on.

After this it assigns the file a 1-150 analytical order which isn't right, so it requires me to edit the sample orders in excel which isn't easy to do as it needs matching to the 1,10,11,12 format as you cannot change file name once imported.

It would be nice to be able to sort the imported data within MS-DIAL GUI interface. Or allow for edit of file names or order.
4
MS-DIAL / Re: CAN NOT download MSDIAL metabolomics MSP spectral kit
Quote from: Amberrr – on
Me and my colleagues couldn't download the 3rd one online database "ESI(+)-MS/MS from standards+bio+in silico (16,995 unique compounds)", while we can download the other three successfully.
It shows "403 Forbidden" on page when we try to download it.

Yes, I face the same issue, so the problem is reproducible. Must be something on the server end here. Minor fix I presume, once we get the developer's attention on it.
5
MS-DIAL / Re: S/N (signal-to-noise) filter in MS-DIAL
Quote from: wdwvt1 – on
Hi all,
I couldn't find an answer for this in this forum or generally online.

MS-DIAL routinely calls peaks like those in the attached screenshot. The average S/N of these peaks is extremely low. I would like to avoid these peak calls altogether: is there a setting in MS-DIALs peak picking/featurization that would allow me to avoid these?
If not, can I filter them out after peak-picking? Is there any place to set a threshold such that any feature with average SN below that threshold is not shown in the alignment?

I can certainly export the data to python and do it there easily, but for quick GUI based processing I would love to be able to do this.

Any advice greatly appreciated.

Thanks,
Will


Hi Will,

I suppose changing the amplitude under peak detection and MSDec tabs would get you the desired results? Does setting a higher cut-off not resolve this issue?

Are these so called peaks above your set noise level?
6
Mass spectrometers / Re: ms dial library problem
Quote from: darlisson – on
Hello, I recently installed MSDial to interpret the chromatographic profile of phenolic extracts from fruit samples. However, on my notebook, I can't buy MS2 spectrum with msdial library. It appears as follows:

I downloaded the library for compounds in negative mode and inserted it as recommended by the tutorial. Also installed MSFinder. However, when I click to search in MS Finder the program closes.
I can check all peaks, but it is impossible to compare with the libraries.
My version is Windows 11 Home Single Language - 21H2.

I face the same issue, perhaps better to use MSDial version 4.9 or higher, but not 5. However, for me even loading libraries in MSFinder does not help as I get no annotations or IDs. Sometimes clicking MSFinder from MSDial crashes them both.
8
MS-DIAL / Re: How to do multiple regression or PCA in MS Dial?
Quote from: triston.groff – on
PLS-DA may be better for this since it is supervised. Anyway, this can be done by assigning Class ID ['option' tab in toolbar],
 normalizing (must assign class first; I prefer LOWESS + an internal standard)[data visualization tab], then doing stats in the tool that is also under the data visualization tab (can't remember name off the top of my head).

Take care,
Triston


Great tip, what I struggle to understand is for PLS-DA it requires a y-variable to be defined, would you know how that's done?
9
MS-DIAL / Peak detection: Amplitude calc
Hi all,

I have been exploring MS-DIAL recently and I am wanting to learn optimising the parameters better. My question is for GCQTOF data, on MSDIAL - during peak detection how do I determine an accurate amplitude? Recommended is 1000, there's not a lot of guidance on the MS-DIAL manual explaining this in detail.

I am used to exploring my raw data in mzMine to determine noise level, in 1E2-5E5 sort of ranges. How does, or does it at all translate to how amplitude is decided?

Thank you
10
MS-DIAL / Re: Injection volume and Y variable
Quote from: Hiroshi Tsugawa – on
Hi,

currently, there is no meaning of injection volume (in the previous version, it was used for calculation of lipid-semi quantitative values).
For Y variable, if you do PLS or OPLS for the discriminant/regression analysis in MS-DIAL, the information is required.

Hiroshi



I am trying to do PLSDA, but I am unsure what I am supposed to put into Y-variable. Any help or direction towards literature please?
11
MS-DIAL / Re: MSDial crashes after processing files and after opening alignment navigator
Quote from: James – on
I have a similar issue, but for me it crashes before ever showing the peak spot viewer.

This only seems to happen when using GC-MS data, and only when loading 10 or more files. I can load and process up to 9 files successfully, but it reliably crashes when loading 10 or more. It doesn't seem to matter what parameters are used or whether any libraries are searched, etc. This is the case with either .mzML or .D files.

I can load at least 20 LC-MSMS files though (and presumably more, but I haven't checked), so maybe the problem is specific to GC-MS processing? What type of data are you using?

James

What libraries are you loading on MS-DIAL for your LC-MS data. For GC there seems to be a lot of help in compound annotation but not as much for LC, I feel. Wondered if your approach may help me use MS-DIAL for LC-MS data too.
12
MS-DIAL / Re: Cannot get file to mgf
Quote from: kim2267 – on
Ive been able to obtain data by inputting either raw files or mzml files but both have failed in being able to output a mgf file from alignment results. Ive been able to only obtain csv or txt files as the export and was wondering how I could troubleshoot this. I've tried looking online if anyone has gone through similar issues but could not find a solution to this issue. Appreciate any help and your suggestions.

Do you get blank file or don't get any file at all? I have had similar issue before and I only got a blank export for mgf, 0KB.
13
MS-DIAL / Re: MS-DIAL 5.1.0 crashing when I try to export the identification results
Quote from: Hiroshi Tsugawa – on
Could you please explain the detail more?
Also, please evalute the following updated version of ms-dial.

http://prime.psc.riken.jp/compms/msdial/download/repository/MSDIAL%20ver%205.1.0.1.zip

Hiroshi

I have but with the latest version 'hard ionisation' option isn't active to be selected. I am using GC-MS data and I can only use 4.9x for GC-MS. Newest version won't let me choose GC-MS or hard ionisation in the first window itself (new project > project path > choose ionisation mode > hard ionisation (unable to select as it is greyed out and radio button not active).
14
MZmine / mzMine parameter optimisation/guidance
Hi all,

Has anyone managed to find a quick guide on how each parameter on mzmine can be optimised based on the data. i.e. what and where to look in the spectra to set min height, or max intensity, or noise threshold values etc.? - or are we all eyeballing it?

I use it mostly for untargeted LC work. GC does not work for me and crashes more often than MS DIAL does.

Thank you
15
MZmine / Re: mzmine chromatogram deconvolution
Quote from: Jan Stanstrup – on
I think the parameters are named slightly differently in mzmine but here is a tutorial for how to estimate reasonable parameters in xcms: https://rawgit.com/stanstrup/XCMS-course/master/1.%20XCMS.html

I know it has been a while since you posted this, but any chance this is still available on another active link? - with time RawGit has been discontinued and therefore I cannot access your resource on that link.

Thank you