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Topic: Exporting CorrDec deconvolution results from the console app (Read 655 times) previous topic - next topic

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, 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.


Re: Exporting CorrDec deconvolution results from the console app

Reply #1
Hi joewandy,

I am currently doing something similar to generate an in-house AMRT spectral library, using the protocol in the SI of (Tada et al, 2019). Essentially, I have created batch scripts to sort data files into compound-specific folders, then create MS-DIAL projects within the folders using the MsdialConsoleApp.exe similar to what you have shown below. MsdialConsoleApp.exe processes files on a per-folder basis, and during this process it creates *.msp2 files within the folder that may be able to be collected using a batch script and then imported to MS-FINDER using MsfinderConsoleApp.exe, but this I am unsure about. I think, though, it is best to view in the GUI even though this is tedious.

From my understanding (though I could be wrong), there are a couple of reasons it is necessary to manually inspect the results in the MS-DIAL GUI application. One is the RT correction from CorrDec; I have had times where my internal standards weren't detected for every sample and I needed to re-process. Another is that, at least for a library, you want to take a spectrum from an injection where the signal is not saturated/too low. Once you determine the optimal spectrum in the dilution series, this can be manually exported into MS-FINDER. If you don't care about choosing the optimal, it is pretty easy to export an entire peak/alignment spot table to MS-FINDER in MSP format. This does awhile, as I have 1600 project files to go through. Once the spectra are imported into MS-FINDER, they can all be exported as MSP or mgf. Maybe you know already know this though.

I had problems viewing the alignment result in the MSDIAL GUI ( v4.80 ) when opening project files created by the MsdialConsoleApp. I read somewhere on this forum that the problem began after v4.48 (starting with v4.6 ), so I started opening the project files with v4.48 GUI and had no more issues.

I have been processing my library files by first converting *.wiff files to *.mzML (performing centroiding with peakPicking ms levels 1- ), then converting the centroided *.mzML files to binary *.abf files. I have noticed that for my reverse-phase files (both *.abf and *.mzML), the data files in MS-DIAL do not have all the features that I can see in SeeMS.. even for the *.mzML files, the intensity is decreased by 10^3 or 10^4 compared to when viewing the same *.mzML files in SeeMS and all of the features are not detected in MSDIAL (I have used minimum peak intensity from 0-1000). I do not have this problem for my HILIC files, which were processed the same way. I would not have noticed this quickly without opening up the project files. Sorry to distract from your issues.. I will probably make a separate thread for this.

Re: Exporting CorrDec deconvolution results from the console app

Reply #2
I recently replied to this thread about assigning Class ID using MsdialConsoleApp, which is semi-related to this topic. Any help on the console app would be helpful to a lot of people I think, so I am attempting to link these unanswered questions.

Take care,