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Detection, identification, and quantitation of an olive allergen using Ettan MDLC, MS/MS, and DeCyder MS

using the PepDetect module of DeCyder MS, where features are detected and quantitated, background intensities are subtracted, and charge states are assigned. Furthermore, the LC-MS data is presented as two-dimensional intensity maps with m/z on the y axis and retention time (RT) on the x axis, as shown in Figure 3. The density of the grayscale pattern confined within the blue boxes is proportional to the signal intensity of a peptide peak at a certain m/z, RT, and charge state, and thus corresponds to full-scan MS data. The red crosses indicate positions (scan numbers) where MS/MS data is available that can be used for identification.

The intensity map in Figure 3 is derived from the same LC-MS data set that generated the base peak chromatogram shown in Figure 2. By comparing the two figures it is clear that the presentation of MS data in the form of an intensity map gives a much better overview of the LC-MS part of the analysis. For example, the signal intensity map clearly shows isotopic distribution of detected peptides, exact retention times, overlapped peptides, and the presence of MS/MS data not directly visible in a base peak ion chromatogram. This type of visualization thus results in a quick overview of the data and can be used to optimize chromatographic and MS conditions, observe unique patterns within the data, or recognize contaminants. At least 1000 ions were detected in each LC-MS analysis of the two allergen samples, which after applying the PepDetect module of DeCyder MS resulted in a final list consisting of ~ 500 deconvoluted and identified peptides.

The next step in the DeCyder MS software analysis was the matching of peptides, from different intensity maps derived from the fractions of Ole_e1_"lite" and Ole_e1_"mer," using the PepMatch module. In this module features from the two allergen samples were compared resulting in relative quantitation of significantly varying peptides. By assuming th
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