| DIA_MS2_fragmentationPeakDetection {IDSL.CSA} | R Documentation |
CSA DIA MS2 Fragmentation Peaks Detection
Description
This function detects fragmentation peaks for the DIA analysis at MS level 2.
Usage
DIA_MS2_fragmentationPeakDetection(DIA_hrms_address, DIA_hrms_file, peaklist,
selectedIPApeaks, massError, smoothingWindowMS1, smoothingWindowMS2,
scanTolerance, nSpline, topRatioPeakHeight, intensityThresholdFragment,
pearsonRHOthreshold, outputDIAeic = NULL, number_processing_threads = 1)
Arguments
DIA_hrms_address |
path to the HRMS file |
DIA_hrms_file |
DIA HRMS file |
peaklist |
IDSL.IPA peaklist |
selectedIPApeaks |
A vector of selected IDSL.IPA peaks only when a number of IDSL.IPA peaks from one peaklist is processed. |
massError |
Mass accuracy in Da |
smoothingWindowMS1 |
Number of scans for peak smoothing in MS1 channel |
smoothingWindowMS2 |
Number of scans for peak smoothing in MS2 channel |
scanTolerance |
a scan tolerance to extend the chromatogram for better calculations. |
nSpline |
number of points for further smoothing using a cubic spline smoothing method to add more points to calculate Pearson correlation rho values |
topRatioPeakHeight |
The top percentage of the chromatographic peak to calculate Pearson correlation rho values |
intensityThresholdFragment |
a value to represent intensity threshold for the fragment at the apex chromatogram scan in MS2 channel |
pearsonRHOthreshold |
Minimum threshold for Pearson correlation rho values |
outputDIAeic |
When 'NULL' DIA EICs are not plotted. 'outputDIAeic' represents an address to save DIA EICs figures. |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe peaklist of co-detected DIA analysis.
References
Fakouri Baygi, S., Fernando, S., Hopke, P.K., Holsen, T.M., Crimmins, B.S. (2021). Nontargeted discovery of novel contaminants in the Great Lakes region: A comparison of fish fillets and fish consumers. Environmental Science & Technology, 55(6), 3765-3774, doi:10.1021/acs.est.0c08507