1
MS-DIAL / Exporting CorrDec deconvolution results from the console app
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