We will move the release distribution from http://prime.psc.riken.jp/compms/msdial/main.html to this repo's GitHub Releases.

• Change the target of FetchVersionDescriptionDocument in VersionUpdateNotificationService.cs from RIKEN to https://api.github.com/repos/systemsomicslab/MsdialWorkbench/releases/latest
• Update the json serialization method for https://api.github.com/repos/systemsomicslab/MsdialWorkbench/releases?per_page=100

Dear MS-DIAL developers,

I am trying to use the MS1 isotopes column in the peak list results to extract the isotopic distribution (M0, M1, M2 ratio).

For MS-DIAL 4.8, I am curious about how the MS1 isotopes data are generated. Specifically, is the isotope data based on only the most intense slice, or is it derived from the average across the entire retention time of the peak?

In the case of MS-DIAL 5.1, I am wondering why the "Isotope region" setting is fixed at 2 Da when exporting the peak list results (refer to the figure) though I can set the region wider in MS-DIAL 4.8. Consequently, only the intensities of M0 and M1 isotopes are displayed, as M2's m/z is slightly above 2 Da. However, to calculate the flux, we require data for all M0, M1, and M2 isotope ratios.

Best,
Zhenwen

Msfinder Console App for Linux version 3.52
outputs the following message and stops.

knishida@DESKTOP-T08EQK0:~/msftmp/msf352lin$ ./MsfinderConsoleApp predict -i Data -o . -m MsfinderConsoleApp-Param.txt
Loading library files..
No usable version of libssl was found
Aborted

Documentation and other information regarding pre-installation of libssl is required.

The current MS-FINDER GUI export TSV format is column-wide like
https://gist.github.com/kozo2/54e4a6ea61fa0989ec15b0f73a90e448 .

We should change it to row-wide like
https://gist.github.com/kozo2/f9dd16b702940e1190635c1010ff5961 .

MS-DIAL version 5.1.230712 have been able to select Normalized data and export the table in the Alignment result export window even for alignment results that are not normalized.

Also, the intensity of the alignment peaks (in the table) are all set to 0.

The "Normalized data *" check boxes should not be selectable (if the result is not normalized).

Input dataset (msp files and parameter file) are attached to this issue.
Data.zip

The two tables here are the "edge list" and the "node table".

Dear developers,
Do you have the plan to update the Linux version, as you know there are a lot of Linux users.
Thanks!

The export of the "Peak list result" has that "peak integration bounds" information.

But the "Alignment result" does not have the "peak integration bounds" information.

We will add a checkbox for the "peak integration bounds" in the Alignment result export window.

Using the graphical version on Windows 11, the program window disappears without an error dialog. Sample size is close to 1000.

Implement the functionality of the red circle in the attached image in MS-DIAL version 5.

version 5.1.230807

The important project parameters are SWATH, lipidomics with .MSP library.

What do you need from me to replicate the problem?

It should state what kind of data we save and where we save it,
and that we do not create/send data where the user's cannot see.

I am creating an issue that was raised on metabolomics-forum.com by user mecolley which I have also experienced myself. Here is a link to the thread: http://www.metabolomics-forum.com/index.php?PHPSESSID=9c325709b3054940eb20c4ac46ee6f8d&topic=1992.0

The issue is that TIMS data causes MS-DIAL version 5 to crash. The OP on the thread I linked mentioned this occurs with .ibf files, but I have experienced this with the raw .d files as well. I can't recall which version exactly, but sometimes I have this occur in some of the version 4.9.xxxx of MS-DIAL. Usually if I struggle long enough troubleshooting, I can get it to process, but it seldom works the first time.

In general, I think MS-DIAL struggles to process timsTOF data. It's not clear if this is on MS-DIAL or Bruker side of things.. I've also had trouble processing TIMS data with other software as well. I have observed this with timsTOF Flex data, and mecolley says this occurs with both timsTOF Pro and timsTOF Flex data. Thanks!!!

Take care,
Triston

Dear MS-DIAL developers,

I am currently using MS-DIAL version 4.90 for GC-MS data processing.
The software crashed during the alignment step. We have noticed that during the peak detection step, some samples have not been run, and if we unticked "Together with alignment" and when we try to open those unrun samples, we get "There is no peak information in 'the sample'. So please select other files or check ion mode for it and re-analyzed it with the ion mode setting". We have tried to lower the "Minimum peak height" to even 10 amplitude, the problem remain.

The weird thing is that when we select a smaller subset (including those unrun samples), it works perfectly. Besides, we can open those files by Chemstation with no problem. which means that the data files should be fine.

Another thing is that when we try different times, different files have problems. Sometimes files A and B have problems, othertimes, files C and D have problems, which makes me quite confused.

in our experience, similar thing happened sometimes but not always.

We also tried Version 4.7, 4.8 and other computers, the problem remains.

Any clue?

Thanks a lot, in advance.

Sukis

Dear MS-DIAL developers,

I would like to use MS DIAL for processing and analysis of a big project where data are confidential. My question is whether the raw data files I upload and the projects I create, are saved in a server or any other space other than locally to my PC?
I run the .exe file every time that I process a dataset. Would it make any difference to install the app - would that make a difference where data are stored? Is there a dosumentation for my question?

My best regards
Katerina

Hello,

I have entered the data in abf format, and the database in msp. But after loading everything and configuring the parameters I don't see any alignment with my database. Also, as you see the bar graph does not look normal, could someone help me? I cant work with this.

Thank you

Dear all,
I am trying to use the last version of MS Dial (vers. 5.1.230517) but once I come to the MS-CleanR peak filtering step, when I click on Apply after putting the different parameters (blank ratio, incorrect mass, RDS, RMD), nothing happens.
Can you please help me?
Thank you!

Hello! I'd like to know, i there is option for alignment results export for FBMN pipeline in GNPS, as there is was such option in older versions?

Hi,
I am using version 5.1.2.231004.
Export of molecular spectrum networking does not work stably.
I repeated this several times. For the majority of the cases MS-Dial dies upon exporting.

Gerd

Hello,

Thanks for your help and your great software :)

I have 2 projects with MSDial ; and for each project, i have 1 "issue" :(

1st project :

This project is based on Windows app. I would like to performed my GCMS treatment with MSDial (4.8) in command line, for optimize my results. For that, i need to have the possibiliy to export the aligned file (Area and Height).
How i can do that ? Actually i just obtain 1 .msdial file per sample. In linux version, i obtain this files, but not in windows.

2nd project :

This project is based on Linux app. For routine treatment, i have one linux server. All data treatment is perfect.
But, when i increase the number of thread, nothing change.
How i can increase that ?

Thanks again for your help,
regards

The following needs to be added.

• Thermo RawFileReaderLicense.doc (and the plain text version).
• Agilent License.rtf (and the plain text version?).
• ???

The export format of MS-FINDER has become row-wide in version 3.6.0.
(We received feedback that the SMILES column was missing from the output.)

However, due to user requests, we will add an option to export the old column-wide format.

how to sent the spectrum of different energy to MS finder in 5.1. In latest version, MS2 can be saved as MSP foramt, but no MS1.

how we bulit a library with different energy in 5.1 version easily?

I will create MsdialConsolelApp.exe for https://github.com/systemsomicslab/MsdialWorkbench/tree/master/src/MSDIAL5.
The folder structure of that project will mimic
https://github.com/systemsomicslab/MsdialWorkbench/tree/master/src/MSDIAL4/MsdialConsoleAppCore .
Thus, the task list (to be implemented) is as follows

High priority

• port of https://github.com/systemsomicslab/MsdialWorkbench/blob/master/src/MSDIAL4/MsdialConsoleAppCore/Process/LcmsDiaProcess.cs
• file exporter for the above

Mid priority

• TBD

Low priority

• TBD

Hi,

I am currently trying to use the MsdialConsoleApp.exe from version 4.9.221218 . I was able to set all the needed parameters in a txt file, however I am not sure how to assign the sample type (Blank/QC/Samples) and the Class id to different the different files in order to analyse biological groups using the method file for the command line (It would be of relevance for various settings in the alignment step).
If there is such possibility to assign it through the method file I would appreciate any help

Thanks a lot

P.S. Thanks for all the effort in making a user friendly Application for Metabolomics/Lipidomics

Sincerely,
Abraham

Hi,

I was wondering if there is a way to export just the MS features contained within a given ms/ms fragment search? If not, is there an alternative approach within the msdial software by which i can mark the compounds found within the ms/ms fragment search prior to exporting the feature list?

I am currently using msdial v 5.1 .23

Thank you,

Warm regards,

Shota.

I am trying to combine MS-DIAL preprocessing and SIRIUS/CANOPUS annotation in one workflow.

For this I take exported .mat spectra from MS-Dial vaersion 5.1.230517 to SIRIUS and want to perform batch processing.

Problem 1)
This bugs since Sirius expects no “null” in case no library annotation was made before.

I sent this to Markus and he wanted to change something on the SIRIUS side and asked me to delete the “null” entries as a workaround. This works but should be reararranged either in MS-DIAL or in SIRIUS.

Problem 2)
I next provide one entry of the .mat output of MS-Dial:
ID=613 is the alignment ID of MSDIAL but it is not separated from the mz mass (640.3454) in the NAME section
and the latter it is not indicated as "precursor mz" .

NAME: Unknown|ID=613640.3454|RT=13.113
PRECURSORMZ: 640.34544
PRECURSORTYPE: [M-H]-
RETENTIONTIME: 13.1132666666667
FORMULA: null
ONTOLOGY: null
INCHIKEY: null
SMILES: null
COMMENT: |PEAKID=613|ISOTOPE=M+0
IONMODE: Negative
MSTYPE: MS1
Num Peaks: 11
640.34544 2605
640.40443 20
641.06957 21
641.34909 893
641.39291 18
641.4231 30
641.69005 17
642.26588 24
642.29664 19
642.34746 184
642.38204 29
MSTYPE: MS2
Num Peaks: 22
122.00124 6
152.99574 17
196.0379 16
214.04885 5
238.04797 4
268.0583 15
281.2483 144
321.15853 2
340.33212 3
413.77283 2
415.28565 3
416.46199 2
421.19309 2
427.44831 3
446.4576 2
455.34643 2
478.29346 56
497.25931 3
520.3027 8
550.31365 4
622.32911 3
640.34624 208

For the corresopnding .tsv output file of SIRIUS after SIRIUS/CANOPUS processing this has the following consequence
614_Mat_2023_06_05_13_47_21_AlignmentResult_2023_06_UnknownID613662.3301RT12.297
for the feature ID.

Note that 614 is the SIRIUSID and ID613 represents the AlignmentID of MSDIAL....

In case MSDial had annotated something, this AlignmentID is replaced be the metabolite name here.
In this case the AlignmentID of MSDial is no longer present in the NAME section, that is the MSDIAL ID would be lost
as information is taken later from the NAME section.
(i.e. the PEAKID is found only under comments throughout all library entiries of the .mat export...)

Using workflows from mzMine to SIRIUS the final FeatureID in SIRIUS is actually a concatenation of
the SIRIUSID+FILENAME +PEAKID of the data source.

I think this should be better aligned between the individual pipelines
starting with the output .mat format of MSDIAL.

Hi,
I am asking for a guidance to operate MS-DIAL ver 4 using a command line in a python code
Thanks,
Nitzan

Bug report:
I have multiple versions of MS-DIAL installed for continuity with different ongoing lipidomics projects. I discovered that a reexported alignment result from one of my projects did not match the export I had originally generated months before. It had the same alignment IDs and metabolite names and such, but reference mass, reference rt, formula, ontology, INCHIKEY, and SMILES were all nonsensical for the listed metabolite name. After some testing, I’ve realized that if you save an MS-DIAL project, load it later and rerun the identification with a different version’s lipid library, the previous alignment result’s IDs will be replaced with lipids from the other version's library, which won’t necessarily correspond to the original IDs. When exporting the alignment parameters, it also replaces the library name, so there’s no record of the original processing and its IDs. This seems to be true for all the versions I’ve been using (4.70, 4.90, and 4.9221218).
Thanks!

This image-equivalent functionality (that existed in MS-DIAL version 4)
will be implemented in version 5.

Hi,

We are currently using Agilent 6545 TOF. Since there are 3 collision energy applied, normally 10, 20, 40V, I am curious which MS/MS spectra will be used by MS-DIAL? Is there any way to select the spectra that I want or even average spectra from all the 3 collision energies?

Thanks in advance.

Sukis

I just recently started using MS-dial as an analysis tool. To use this I want to use the authentic standards available on the website as a reference but after downloading both positive and negative, I have been unable to install them. The following notification always pops up as also can be seen in the attachment: "This patch package could not be opened. Contact the application vendor to verify that this is a valid Windows Installer package". Is there any way to solve this problem?

Regards,
Arne

Hi All,
I would like to highlight an important issue I recently faced, especially for EAD identification.
I am processing exactly the same sample which were acquired with sciex zeno tof 7600 DDA with EAD fragmentation.
In the version 5.1.230222 many PE lipids were identified however in version 5.1230807 they are all gone. (Slide 1) I can see some of the PE species only if I click suggested. I can share the files and open for discussion.
Thanks for your time.
Best.
Cagakan

MSDIAL 5 problem.pptx

In particular, the console version has no formula information at all in the structural prediction.

MS-finder fails to start when system display language in Windows 10 is set to polish. Works fine when it's set to english. Ms-dial doesn't have this problem.

Hi all,

I plan to use medial command line to do alignment since I have too many samples. But I have 2 questions.

1. How to specify the order of the sample sequence in ms-dial command line in the parameter setting? The sequence of the output file looks randomly but I want to set the file type and class of each sample.
2. I have added map file in parameter setting which is shown in the attached photo. But how to make sure the msp file is used and the compound ID managed in the output msdial file from command line.

Thank you very much!

The ms-dial program calculates several scores to estimate the peak quality, and it is used for deconvolution actually.
However, there is no export function for the scores so that users can evaluate.
(So I will add an export function for it).

Reference

• MetaClean: A Machine Learning-based Classifier for Reduced False Positive Peak Detection in Untargeted LC–MS Metabolomics Data in the journal named Metabolomics.

Discussed in #118

In an environment with Ubuntu version 22.04, the following issue occurs.
Installing the libssl-dev package does not resolve it.
On the other hand, in an Ubuntu 20.04 environment,
MsdialConsoleApp works even if the libssl-dev package is not installed.

./MsdialConsoleApp lcmsdda -i ./LCMS_DDA/ -o ./LCMS_DDA/ -m ./LCMS_DDA/Msdial-lcms-dda-Param.txt -p
Loading library files..
Start processing..
./LCMS_DDA/Nega_Ida_QC_1_1.mzML
Reading data...
No usable version of libssl was found
Aborted

Hi!
It seems we need some help with MS-DIAL software, Windows version.
The attached file is a screenshot from version 5.1.230517 and when we press the "Next" button on that screen the program thinks for some seconds then closes without any error messages. We also have tried version 4.9.221218 but the effect was similar. The computer where it all happens has 32 Gb RAM, last generation of i7 CPU, lots of free disk space and Win10 Pro. Turning off the antivirus software does not help.
My colleague runs the software successfully on a similar computer. Can you suggest any ways to solve the problem?

Thank you in advanced!

Dear all,
When I export normalised data from MS-DIAL, the output .csv file often appear in a confused format.

When I export normalised Area data, for a sample, each cell of the corresponding column should represent the lc-ms area corresponding to a substance of it, but in the data I exported, other sample names, FALSE, -1, data with ':' and so on are often appeared in the column, which is strange. A simple example is shown below.

average RT average MZ sample1 sample2
8.879 335.04319 80485.7791564993 92384.1259323545
25.266 112.986 6907.01276694368 -1
2.023 244.96782 A6.22.3.1 28173.6231583602
12.165 282.06686 FALSE 6.817:1000.39108

What is the reason for these confusing formats? Can you please help me?
Thank you very much!

I will maintain the ChangeLog for

• MS-DIAL version 5 series
• MS-FINDER

Dear MS-DIAL developers,

I would need some of your help to understand the 'total score' in the exported alignment result.
I read the tutorial and the publication about the equations and how the total similarity is calculated with all four scores.
In my exported files (please see an example attached) I see the 'RT similarity', 'm/z similarity' and the dot and reverse dot products used for the MSMS similarity but I do not see the isotope ratio similarity column. Why is that please?
Another thing I am struggling with, is how to interpret the total score column. What would be the 'perfect' similarity score when using all four scores, like in this example here?
I get, for example, in the total score column a value of 1.64, how can I interpret this, if this is a high score or not?
exported alignment result.xlsx

Thank you and best regards
Katerina

Hi,

Is there any dummy .wiff available for testing? I am using the current version of MS-Dial. But, couldn't find any demo folder for mass spectrometry data. Any link/reference of the archive in the README.md would be highly helpful!

Thanks!