DIA analysis by IDSL.CSA
The Data-Independent Acquisition (DIA) peak processing approach embedded in the IDSL.CSA software can perform MS2 peak deconvolution on the MS1 peaks detected by IDSL.IPA. First, the fragmentation ion seeds are identified from the nearest raw MS2 chromatogram scan to the MS1 scan at the apex of MS1 chromatographic peaks. The MS1 and MS2 chromatograms are subjected to a two-step smoothing process, utilizing the LOESS function followed by cubic spline smoothing, aimed at increasing the number of points and reducing the jaggedness of the peaks. Pearson's correlation coefficients of the chromatograms of MS2 fragmentation peaks are calculated with respect to MS1 chromatogram peak. Finally, the mass of the MS1 chromatogram peaks as precursor value and correlating MS2 ions with the MS1 ion as fragmentation spectra are exported in a standard MSP format.
This DIA chromatogram deconvolution approach is also capable of automatically detecting Sequential Window Acquisition of All Theoretical fragment ion spectra (SWATH-MS) DIA data types through the utilization of offset information present in the metadata of mass spectrometry files. In the absence of offset information, the IDSL.CSA DIA defaults to the All-Ion Fragmentation (AIF) data analysis mode.
MS2 SWATH-MS scan usually are distibuted across many scans in compare to the MS1 scans; therefore, we suggest using higher smoothing windows for MS2 scans. For example, if smoothing window for MS1 was set at 25 MS1 scans, the smoothing window for MS2 scans can be set at 500 MS2 scans.
Ex: Chromatogram deconvolution for Tryptophan in a the MSV000090242 study
Hint: The spectral entropy (S) values are different between IDSL.CSA/DIA peak deconvolution and IDSL.FSA peak annotation because a 1% noise removal was applied in the spectra annotation step.
Ex: Chromatogram deconvolution for Rutin in a the MSV000087782 study
