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Messages - Ondrej

2
MS-DIAL / Re: Search lbm2 file
Hi,
lbm2 is just a binary form of the msp library, to speed things up. You can build your own msp from LipidBlast if needed.
O.
3
MS-DIAL / gap filling problem
Hi,
I am testing MS-DIAL v 5.1.230222 and I found a problem with "Gap filling by compulsion" option.

Quote
Gap filling by compulsion: If you check this, the peak recognition is performed by the average peak width of samples having the metabolite feature even though no local maximum is observed in the chromatogram. This is validated by default.

I do not want it, I switched it OFF.
However, there is peak intensity and peak area value even in case of BLANK, where there is no peak / data at all (see attached image).
It should not be there.
O.
4
MS-DIAL / benchmark ver 4.9.221218 vs 5.1.230222
Hi,
I processed an identical set of metabolomics data using identical parameters either in ver 4.9.221218 or ver 5.1.230222.

MS-DIAL 4.9.221218 processed 164 files in 7 minutes (from the first "dcl" file to last) and saved the alignment file in next 6 minutes.
Total 13 minutes.

MS-DIAL 5.1.230222 processed 164 files in 20 minutes (from the first to the last) and I canceled the alignment after 60 minutes (CPU at constant ~6.6% and slowly increasing allocated memory ~14.2 GB).
Total 20 + 60...

Update, after fresh restart:
MS-DIAL 5.1.230222 processed 164 files in 19 minutes (from the first to the last) and finished the alignment in 2 hours and 11 minutes.
Total 2 h 20 min.
O.

6
MS-DIAL / Nomenclature of oxidized lipids (LipidBlast)
Dear Hiroshi,
could you please unify the LipidBlast nomenclature with the recommended format?
(DOI 10.1194/jlr.S120001025, Liebisch et al. JLR, 2020)

I am using MS-DIAL v4.90 (Windows) and the main problem is with the reported oxygens. Using LM notation the 'position' should be before the "O" and the number of oxygens after the "O".

MS-DIAL name is: PI 17:0_18:2;2O
The normalized name at this level should be: PI 17:0_18:2;O2

MS-DIAL: SM 42:2;2O
LipidMaps: SM 42:2;O2

MS-DIAL: ST 29:2;O;S
LipidMaps: ST 29:0;O

Thank you,
Ondrej
7
MS-DIAL / MrmprobsConsoleApp parameters
Hi Hiroshi,
would it be possible to add a command line option to export the raw matrix data file?
Thank you.
Ondrej

Code: [Select]
Mrmprobs Console App requires the following args:
                                                MrmprobsConsoleApp.exe <analysisType> -i <input folder> -o <output folder> -m <parameter file> -r <reference library file> -d <dia dictionary file (required in abfdia)>
                                                Where: <analysisType>   is one of abfmrm, mzmlmrm, mzmlscan, abfscan, abfdia    (required)
                                                           <input folder>       is the folder containing the files to be processed      (required)
                                                           <output folder>      is the folder to save results   (required)
                                                           <method file>        is a file holding processing properties (required)
                               <reference library file>           is a file containing rt/transition/ratio/range information at tab-delimited text.
                               <dia dictionary file>    is required in DIA-data process containing SCAN/DIA ScanID MzBegin MzEnd information as tab-delimited text
8
MS-DIAL / MRMPROBS 2.60 view/edit data export problem
Hi Hiroshi,
I found a possible bug. I have one peak close to my analyte RT. When my analyte is not present, MRMPROBS selects the wrong peak nearby. As expected.

Now I want to manually remove the wrong peak.
If I do it in the "View" mode using left and/or right mouse button, raw data matrix shows the value or N.D. Fine.

If I do it in the "Edit" mode and I select no peak, raw data matrix still shows the previous (last) value. And it should be N.D. as above.
Best,
Ondrej
10
MS-DIAL / Re: when linux version of MS-DIAL will be released
Hi Yuki,
thank you for the alpha version.
I have a blank + 3 abf files, lcmsdda.
  • Win GUI MS-DIAL 4.36 works fine
  • Win console MS-DIAL 4.36 works only with tutorial param file. If I export the params from v4.36, it doesn't work.
  • Linux console alpha does not work. Log is pasted below.
.
Problems
  • Paths. It seems that linux app doesn't parse the paths correctly. I had to use absolute paths to run it and the output is in the root instead of the output folder. Also the file names contain path (see ls output below)
  • Blank - when I set a blank filtering, I can't set blank file. I assume this was not implemented yet.
  • MSPs - I can't upload my MSP. I assume only included libraries are supported now.
  • Params - I have to use a simple param file from the demo files or edit the full version exported from MS-DIAL. Most probably MSP and 'blank' definition problem.
Best regards,
Ondrej

Code: [Select]
./MsdialConsoleApp lcmsdda -i /home/ondrej/MsdialConsoleApp_linux-x64/data/ -o /home/ondrej/MsdialConsoleApp_linux-x64/out/ -m /home/ondrej/MsdialConsoleApp_linux-x64/data/Msdial-lcms-dda-Param.txt -p
Loading library files..
Start processing..
/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\blank.msdial

Deconvoluted peak count: 2990

/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S1.msdial

Deconvoluted peak count: 6477

/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S2.msdial

Deconvoluted peak count: 6611

/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S3.msdial

Deconvoluted peak count: 6525

/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf finished
Joint aligner finished
Reading data...
0 finished
Reading data...
1 finished
Reading data...
2 finished
Reading data...
3 finished
Start finalization
Calculating basic properties
End finalization
Start aligned eic
End aligned eic
Gap filling finished
Finalization finished
Now saving the project to be used in MSDIAL GUI...

strange files
Code: [Select]
ls -alF
total 60548
drwxrwxr-x 2 ondrej ondrej     4096 říj 30 09:54  ./
drwxrwxr-x 4 ondrej ondrej    24576 říj 30 09:54  ../
-rw-rw-r-- 1 ondrej ondrej   738521 říj 30 09:54 '\AlignResult-20201030953.arf2'
-rw-rw-r-- 1 ondrej ondrej   374618 říj 30 09:54 '\AlignResult-20201030953.dcl'
-rw-rw-r-- 1 ondrej ondrej 19111850 říj 30 09:54 '\AlignResult-20201030953.EIC.aef'
-rw-rw-r-- 1 ondrej ondrej  6066618 srp 25 09:38  blank.abf
-rw-rw-r-- 1 ondrej ondrej     4704 zář 17 07:38  LIBneg_FAs.msp
-rw-rw-r-- 1 ondrej ondrej     1535 srp 21  2017  Msdial-lcms-dda-Param.txt
-rw-rw-r-- 1 ondrej ondrej  4819494 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_0.pll'
-rw-rw-r-- 1 ondrej ondrej  4929846 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_1.pll'
-rw-rw-r-- 1 ondrej ondrej  4917734 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_2.pll'
-rw-rw-r-- 1 ondrej ondrej  4923190 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_3.pll'
-rw-rw-r-- 1 ondrej ondrej     8745 říj 30 09:54  Project-20201030953.mtd2
-rw-rw-r-- 1 ondrej ondrej  5313579 srp 25 09:38  S1.abf
-rw-rw-r-- 1 ondrej ondrej  5509016 srp 25 09:38  S2.abf
-rw-rw-r-- 1 ondrej ondrej  5222554 srp 25 09:38  S3.abf
11
MS-DIAL / Re: Question about MRMPROBES
Hi,
it was created for targeted (MRM) analysis. You can run the statistics and quant in excel or use the implemented internal standard approach.
Scan or DIA mode allows you to dissect 'raw' data from the file. We use it for pseudoMRMs (parent > parent) and you can review all samples in parallel (similar to Skyline).
Best,
Ondrej
12
MS-DIAL / MRMPROBS 2.50 max integer problem
Hi Hiroshi,
I found a problem in MRMPROBS 2.50 when the peak is very high.
With some peaks, we reach the limit of 32-bit integer (ranges from -2,147,483,648 to +2,147,483,647).
I see the peak height well, but when I change the info to peak area, I get a negative value.
Thus, when exported as raw matrix, I get zero values.
Could you please change it to 64 bit integer? Thank you.
Ondrej

13
MS-DIAL / Re: Show ion table
Hi Hiroshi,
thank you. It works now.
Tested on two different projects, 25k and 35k peak spots from 350 samples.
The bar grows slowly and then jumps several times till 100%.
Ondrej
14
MS-DIAL / Show ion table
Hi Hiroshi,
I have a problem with "Show ion table" function.
I am not able to use it in some projects. Let's say I have ~800 peaks spots (Blank+, MS2 acquired+, Suggested+) that I need to review.
When I click on the icon, the progress bar "Progress of preparing alignment spot table viewer" stops at random position and never reaches the end. Sometimes is freezes at ~20%, sometimes at ~80%. I can use the X to close the bar and try again.
HW resources are available.
If I completely rebuild the project, it helps sometimes, but sometimes it freezes again. True for multiple versions of MS-DIAL.
Could you please suggest how to find what is wrong?
Thank you,
O.
15
MS-DIAL / Re: Processing of big datasets
The TMP folder within the project folder. Usually something like
project_2020_9_9_12_33_13_tmpFolder
...
peaklist_101.pll
peaklist_100.pll
peaklist_10.pll
peaklist_1.pll
peaklist_0.pll
...