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MS-DIAL / MS-DIAL on Supercomputer Failed to Annotate Metabolite
I was trying to use supercomputer to run MS-DIAL, it successfully produced a peak table, but no peak was annotated even though locations of libraries were provided in the parameter file (i.e., all rows of column "Metabolite name" are "Unknown"). Has any one used command-line version to annotate metabolites successfully? I will very much appreciate it if anyone can help me out.
Following is the content of the parameter file I used:
```
MS-DIAL ver. 4.48
#Project
MS1 Data type Centroid
MS2 Data type Centroid
Ion mode Positive
Target Metablomics
Mode ddMSMS
#Data collection parameters
Retention time begin 0
Retention time end 100
Mass range begin 0
Mass range end 2000
MS2 mass range begin 0
MS2 mass range end 2000
#Centroid parameters
MS1 tolerance 0.01
MS2 tolerance 0.025
#Isotope recognition
Maximum charged number 2
#Data processing
Number of threads 10
#Peak detection parameters
Smoothing method LinearWeightedMovingAverage
Smoothing level 3
Minimum peak width 5
Minimum peak height 1000
#Peak spotting parameters
Mass slice width 0.1
Exclusion mass list (mass & tolerance)
#Deconvolution parameters
Sigma window value 0.5
MS2Dec amplitude cut off 0
Exclude after precursor True
Keep isotope until 0.5
Keep original precursor isotopes False
#MSP file and MS/MS identification setting
MSP file /blue/djlemas/xinsongdu/jupyter_notebook/projects/milkmetabolomics-humanbovine/data/design_files/MSMS-Pos-MassBank.msp
Retention time tolerance 100
Accurate mass tolerance (MS1) 0.01
Accurate mass tolerance (MS2) 0.05
Identification score cut off 70
Using retention time for scoring False
Using retention time for filtering False
#Text file and post identification (retention time and accurate mass based) setting
Text file /blue/djlemas/xinsongdu/jupyter_notebook/projects/milkmetabolomics-humanbovine/pos_msdial.txt
Retention time tolerance 0.1
Accurate mass tolerance 0.01
Identification score cut off 85
#Advanced setting for identification
Relative abundance cut off 0
Top candidate report False
#Adduct ion setting
[M+H]+
#Alignment parameters setting
Reference file /blue/djlemas/xinsongdu/jupyter_notebook/data/metabolomics/Human_Bovine/mzML/demo/QE2_jdg_242_Lemas_1[NeatQC]p.mzML
Retention time tolerance 0.05
MS1 tolerance 0.015
Retention time factor 0.5
MS1 factor 0.5
Peak count filter 20
N% detected in at least one group 0
Remove feature based on peak height fold-change True
Sample max / blank average 5
Sample average / blank average 5
Keep identified and annotated metabolites True
Keep removable features and assign the tag for checking True
Gap filling by compulsion True
#Tracking of isotope labels
Tracking of isotopic labels FALSE
#Ion mobility
Ion mobility data FALSE
```