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czbiohub-sf / Rapid-QC-MS

Realtime quality control for mass spectrometry data acquisition
https://czbiohub-sf.github.io/Rapid-QC-MS
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Parse MS-DIAL settings into parameters file #32

Closed wasimsandhu closed 2 years ago

wasimsandhu commented 2 years ago

Here is a template parameter file that uses a CSV text file.

ls#Data type
MS1 data type: Centroid
MS2 data type: Centroid
Ion mode: Negative
DIA file: 

#Data collection parameters
Retention time begin: 0
Retention time end: 100
Mass range begin: 0
Mass range end: 2000

#Centroid parameters
MS1 tolerance for centroid: 0.008
MS2 tolerance for centroid: 0.01

#Peak detection parameters
Smoothing method: LinearWeightedMovingAverage
Smoothing level: 3
Minimum peak width: 3
Minimum peak height: 35000
Mass slice width: 0.1

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

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

#Text file and post identification (retention time and accurate mass based) setting
Text file: /mnt/storage/samba/shared/metabolomic/MsdialParam/DDA_HILIC_Neg/InternalStandardsNeg.txt
Retention time tolerance for post identification: 0.3
Accurate ms1 tolerance for post identification: 0.008
Post identification score cut off: 85

#Alignment parameters setting
Retention time tolerance for alignment: 0.05
MS1 tolerance for alignment: 0.008
Retention time factor for alignment: 0.5
MS1 factor for alignment: 0.5
Peak count filter: 0
QC at least filter: True

Here is a template parameter file that uses MSP instead:

ls#Data type
MS1 data type: Centroid
MS2 data type: Centroid
Ion mode: Negative
DIA file: 

#Data collection parameters
Retention time begin: 0
Retention time end: 100
Mass range begin: 0
Mass range end: 2000

#Centroid parameters
MS1 tolerance for centroid: 0.008
MS2 tolerance for centroid: 0.01

#Peak detection parameters
Smoothing method: LinearWeightedMovingAverage
Smoothing level: 3
Minimum peak width: 3
Minimum peak height: 35000
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: /mnt/storage/samba/shared/metabolomic/MsdialParam/DDA_HILIC_Neg/urineNeg.msp
Retention time tolerance for identification: 0.4
Accurate ms1 tolerance for identification: 0.01
Accurate ms2 tolerance for identification: 0.015
Identification score cut off: 70

#Alignment parameters setting
Retention time tolerance for alignment: 0.05
MS1 tolerance for alignment: 0.008
Retention time factor for alignment: 0.5
MS1 factor for alignment: 0.5
Peak count filter: 0
QC at least filter: True