This function detects fragmentation peaks for the Composite Spectra Analysis (CSA) using IDSL.IPA peaklists.
CSA_fragmentationPeakDetection(CSA_hrms_address, CSA_hrms_file,
tempAlignedTableSubsetsFolder = NULL, peaklist, selectedIPApeaks = NULL,
RTtolerance, massError, minSNRbaseline, smoothingWindowMS1, scanTolerance, nSpline,
topRatioPeakHeight, minIonRangeDifference, minNumCSApeaks, pearsonRHOthreshold,
outputCSAeic = NULL)A dataframe peaklist of co-detected CSA analysis.
path to the HRMS file
CSA HRMS file
tempAlignedTableSubsetsFolder
IDSL.IPA peaklist
A vector of selected IDSL.IPA peaks only when a number of IDSL.IPA peaks from one peaklist is processed. When `NULL` is selected, the entire peaks in the peaklist are processed.
retention time tolerance to detect common peaks
Mass accuracy in Da
A minimum baseline S/N threshold for IDSL.IPA pseudo-precursor m/z
number of scans for peak smoothing.
a scan tolerance to extend the chromatogram for better calculations.
number of points for further smoothing using a cubic spline smoothing method to add more points to calculate Pearson correlation rho values
The top percentage of the chromatographic peak to calculate Pearson correlation rho values
Minimum distance (Da) between lowest and highest m/z to prevent clustering isotopic envelopes
Minumum number of ions in a CSA cluster
Minimum threshold for Pearson correlation rho values
When `NULL` CSA EICs are not plotted. `outputCSAeic` represents an address to save CSA EICs figures.
[1] Fakouri Baygi, S., Kumar, Y., Barupal, D.K. (2022). IDSL.IPA Characterizes the Organic Chemical Space in Untargeted LC/HRMS Data Sets. Journal of Proteome Research, 21(6), 1485-1494, tools:::Rd_expr_doi("10.1021/acs.jproteome.2c00120")
[2] 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, tools:::Rd_expr_doi("10.1021/acs.est.0c08507")