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1
MS-DIAL / MS-DIAL Crashing when I add .txt file for Identification
Last post by afouche -
Hello,

We have been building a compound library in-house to use with our metabolomics methods, and are at the point where we would like to use the library in MS-DIAL for data analysis. When our library is loaded into MS-DIAL none of the following information populates: Metabolite Name, Formula, InChIKey. The library is in MSP format, and should have all of this information present.

In an attempt to at least get metabolite names to populate, I tried to add a .txt file with metabolite name, MS1 m/z, and RT values for identification; however, each time I try to load a .txt file into the program, it crashes. The program closes itself out, and the project is saved with the same parameters as before the .txt file was added. To try and stop this from happening, I loaded the project with no advanced identification settings. Once loaded, I went back to Identification parameters and added the .txt file, but MS-DIAL still crashed.  I have tried reinstalling MS-DIAL, which has also not helped.

Has anyone else had issues loading their method specific MSP libraries into MS-DIAL?

I have tried this with as few as 1 sample and 1 blank at a time. The files being analyzed in MS-DIAL are in mzML format, converted from .raw using ProteoWizard. The data was collected on a Thermo Orbitrap Exploris 120.


Any guidance is appreciated!

Thank you,
Angelique
3
MS-DIAL / Undocking panes option?
Last post by ale.cohen1 -
Given the multiple panes and complex datasets, it would be VERY helpful if the panes within MS-DIal could be undocked or 'floating' to make better use of screen realstate with dual monitors :) Pleaaaaseee

Cheers

Alejandro
4
MS-DIAL / Re: Issues with data processing in MS dial
Last post by James -
I don't have a good solution, but wanted to say that I also have this issue for GC-MS data. It seems to crash at some point before showing the peak spot viewer or creating any .mtd2 file about 9 times out of 10 - but every so often, after stubbornly fiddling with the parameters and re-attempting, the alignment works and the peak spot viewer pops up.

I have not figured out which parameters, if any, are actually important for getting it to work. Several times I have thought I discovered the secret, only for the next analysis to crash again - and again and again.

I have accepted the stochasticity of getting MSDial to work and figure it is better to indulge my gambling habit here than at the slot machines, but would certainly appreciate a solution if you or anyone else has figured it out.
5
MS-DIAL / CCS calibration for TWIM-MS using EDC method
Last post by MaxFeuerstein -
Dear Hiroshi and MS-DIAL team,

I was working with Waters travelling wave ion mobility data recently and was happy to realize that MS-DIAL treats TWIMS data.
However, I am curious if you could integrate an alternative option for the TWCCSN2 calibration?

Instead of using coefficients A, exponent B and t0 an alternative method is typically used using a m/z dependent correction factor to determine the "corrected arrival times" tc from arrival times ta by taking into account the "EDC (Enhanced Duty Cycle) delay coefficient" C, which is an instrument dependent parameter (you find it in the .raw data folder in the methods).
I think this is the approach typically used in Waters DriftScope and would be a nice as an option and often you use DriftScope to overwrite the initial mobcal.csv file with the new calibration function.

You can find the details here:
https://www.nature.com/articles/nprot.2008.78

Until now I re-calculated CCS from arrival times using this approach which is not too time consuming, but automation would be nice and not all users will be aware on these differences.

Thanks a lot for the great work and best regards,

Max
8
Mass spectrometers / Re: Cloud Plot - XCMS
Last post by lbutkovich -
Hi, I'm also struggling to use the Cloud Plot output in XCMS. I would really like to use this tool for processing the large amounts of data I'm working with, but there are a few issues. When I compare the Cloud Plots to the peaks of interest that I can visually see when I load up the TIC plot on MZmine, I cannot recapitulate the m/z and RT of my peaks of interest! Additionally, the 'table view' of the XCMS cloud plot is not working for me.

If anyone can give feedback for me on this, it would be much appreciated. Otherwise, is there advice for other LC-MS and LC-MS/MS data analysis tools to try? So far, I've used the GNPS LC-MS/MS data processing tool to generate Cytoscape networks and excel sheets with data. This is helpful, but also a lot of info that is difficult to filter through. I have also used MZmine to manually look at the TICs.

Thanks in advance,
Lazarina Butkovich
Grad student at UCSB
9
MS-DIAL / Retention Time similarity score in MSDIAL
Last post by cagakan -
Hi All,
I have a quick question. I am struggling to understand how the RT similarity function of MSDIAL is working. Do we need to use the same gradient explained in `A lipidome atlas in MS-DIAL 4` article?
If we didn't use the same gradient does it make any sense do use the Retention time similarity function?
Have all the retention time data embedded to `Msp20210527163602_converted.lbm2` from the paper?
Thanks for your help!
Cheers.
Cagakan
10
MS-DIAL / Re: Smoothing parameter
Last post by spapaz -
For what I understood, the "smoothing level" is the number of data points that will be considered in function (e.g. moving average).
E.g. Smoothing level 3 = 3 data points. It would be nice if someone can confirm that´s the case in MS-DIAL.
Also, because for my basic understanding of the smoothing function, the number of data points should always be kept odd (e.g. 3, 5..) in order to maintain signal symmetry.

Can someone comment ?

Stefano