DDA analysis by IDSL.CSA
In tandem mass spectrometry (MS/MS) analyses, multiple MS2 DDA scans with similar precursor values may often be present within a single MS1 chromatographic peak, which can lead to challenges in identifying and quantifying the compounds of interest. To address this issue, the IDSL.CSA/DDA approach was developed to perform Data-Dependent Acquisition (DDA) analysis using MS1 chromatographic peaks through three different methods. The first method involves selecting the most abundant MS2 DDA spectra with similar precursor m/z values across the MS1 chromatographic peak. The second method integrates the MS2 DDA spectra with similar precursor m/z values. The third method filters ions from MS2 DDA scans with similar precursor m/z values through the DDA0014 parameter in the DDA tab of the IDSL.CSA parameter spreadsheet. For instance, a chromatographic peak for kynurenine and its associated MS2 DDA scans (with PrecursorMZ = 209.0926) are shown below as an example.
This option involves selecting the most abundant DDA scan with a similar precursor mass as the representative of the MS2 DDA scan for the MS1 chromatographic peak. In this case, DDA scan 3 is the most abundant and is selected as the representative.
This option involves integrating all MS2 DDA scans with similar precursor masses that fall within the boundaries of the MS1 chromatographic peak to generate an integrated MS2 DDA spectra. To illustrate, the figure below shows an integrated spectra resulting from combining all MS2 DDA scans for kynurenine.
This option employs a filtering mechanism to remove non-correlating peaks from multiple MS2 DDA spectra with similar precursor m/z values within the MS1 chromatographic peaks. This generates a refined DDA spectra that improves the accuracy and reliability of the analysis. To implement this option, there must be at least 3 related MS2 DDA spectra with similar precursor m/z values within the boundaries of the MS1 chromatographic peak. however, the Selection of the most abundant DDA spectra method is still used when DDA scan counts is <= 2. After detecting more than 3 DDA scans, a peak alignment table is generated for the MS2 m/z values of these DDA scans, and the percentage of frequency of m/z peaks is calculated on the alignment table. The relative standard deviations for the aligned m/z are then calculated to remove constant noisy peaks. Finally, Pearson’s correlation coefficients are computed to detect MS2 m/z peaks with similar trends. An example of the ion-filtered DDA spectra obtained from DDA spectra with similar precursor m/z values for kynurenine is presented in the figure below.
