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Messages - joewandy

1
MS-DIAL / Exporting CorrDec deconvolution results from the console app
Dear Hiroshi and team,

Thank you for your hard work in developing and supporting this app. It's hugely valuable for our work. I have a problem with using MS-DIAL that I hope you could help.

Is there any way to run MS-DIAL CorrDec deconvolution from the console app and then export the identified peak list and spectra as .msp file? I would like to script MS-DIAL to process a large number of files, so it would really help if we can do this.

I saw this post http://www.metabolomics-forum.com/index.php?topic=1473.msg4376#msg4376, but that's for the GUI app. I'm not sure if it's possible from the console app?

I'm running MSDIAL ver.4.80 OSX, and below is my config file.
Code: [Select]
#Data type
MS1 data type: Centroid
MS2 data type: Centroid
Ion mode: Positive
DIA file: /path/to/AIF_MSDIAL_TEMPLATE.txt

#Data collection parameters
Retention time begin: 0
Retention time end: 100
Mass range begin: 70
Mass range end: 1100

#Centroid parameters
MS1 tolerance for centroid: 0.01
MS2 tolerance for centroid: 0.0025

#Peak detection parameters
Smoothing method: LinearWeightedMovingAverage
Smoothing level: 3
Minimum peak width: 5
Minimum peak height: 1000
Mass slice width: 0.1

#Deconvolution parameters
Sigma window value: 0.5
Amplitude cut off: 0

#Adduct list
Adduct list: [M+H]+

#MSP file and MS/MS identification setting
MSP file: /path/to/msp_file.msp
Retention time tolerance for identification: 100
Accurate ms1 tolerance for identification: 0.01
Accurate ms2 tolerance for identification: 0.05
Identification score cut off: 70

#Text file and post identification (retention time and accurate mass based) setting
#Text file: 
Retention time tolerance for post identification: 0.1
Accurate ms1 tolerance for post identification: 0.01
Post identification score cut off: 85

#Alignment parameters setting
Retention time tolerance for alignment: 0.05
MS1 tolerance for alignment: 0.0015
Retention time factor for alignment: 0.5
MS1 factor for alignment: 0.5
Peak count filter: 0
QC at least filter: True

#CorrDec setting
CorrDec excute: TRUE
CorrDec MS2 tolerance: 0.01
CorrDec minimum MS2 peak height: 500
CorrDec minimum number of detected samples: 4
CorrDec exclude highly correlated spots: 0.9
CorrDec minimum correlation coefficient (MS2): 0.9
CorrDec margin 1 (target precursor): 0.1
CorrDec margin 2 (coeluted precursor): 0.1
CorrDec minimum detected rate: 0.7
CorrDec minimum MS2 relative intensity: 1
CorrDec remove peaks larger than precursor: FALSE


Any help here would be much appreciated! Thanks.

Joe
3
MS-DIAL / Re: Command-line questions
Hi MSDIAL team and all,

It seems that point 1 above has been fixed in the latest version (v.4.24). If somebody could help with 2 and 3 above, that would be great. Thanks.
5
MS-DIAL / Command-line questions
Hi Hiroshi and team,

I'm running MSDIAL  (v4.12) terminal version in a script as part of my automated workflow. I was getting stuck and have a few questions that hopefully you could help with. Thanks a lot in advance!

1. I can't get the compound identification working from MSDIAL terminal version.

In the method file, I have specified the path to an MSP file, however I don't see any compound annotations at all in the resulting .msdial file. I assumed that compound annotations would be indicated in the 'Title' and 'Dot product' columns of the .msdial file, is that correct?

I've attached a zip file containing method file, the msp file and the output msdial file. The same files when used with the GUI worked fine. Any chance you could take a look, that would be great.

2. Would it be possible to run the CorrDec method from the terminal? I don't see any option to specify that in the method file.

3. Can I export a peak list as .msp format from MSDIAL terminal version, instead of getting the .msdial output? This would be similar to doing to Export > Peak list result from the GUI. That would give a quick way to see the identified compounds and their spectra.

Have a nice day, and thank you so much for your help.
Joe
6
MS-DIAL / Can't process mzML file in DIA mode using the latest version of MSDIAL
Dear MSDIAL developers,

When using the latest version of MSDIAL (4.24) I received the following error when trying to process an mzML file in DIA mode.

Quote
MsdialConsoleApp.exe lcmsdia -i data -o data -m data\Msdial-lcms-dia-Param.txt
Loading library files..
Start processing..
Could not load file or assembly 'MsdialCommon, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null'. The located assembly's manifest definition does not match the assembly reference. (0x80131040)

However if I revert to an older version of MSDIAL (4.12) this works:

Quote
MsdialConsoleApp.exe lcmsdia -i data -o data -m data\Msdial-lcms-dia-Param.txt
Loading library files..
Start processing..
data\StdMixHigh_DIA1_P1-C-2_01_5747.mzML
end peak picking
Exporting peak list data: data\StdMixHigh_DIA1_P1-C-2_01_5747.msdial

Deconvoluted peak count: 513

data\StdMixHigh_DIA1_P1-C-2_01_5747.mzML finished
Finished

The params files that I used are attached in this post. I can't include the mzML because it's too big, but I believe this problem happens for all mzML files.

I know the documentation says that the DIA mode 'accepts ABF format file only', so I'm very happy to find out that I could use an mzML file directly with an older version of MSDIAL. However it would be good if it works with the latest version too.