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*   Matrix Conversion
Some processing utilities, such as Baseline Correction and Noise Elimination, Smoothing, and the JCD Component Detection Algorithm, use internal matrix calculations. For high resolution/accuracy data, how the matrix is created can have a significant influence on the outcome of the processing utilities.
For additional information, see Baseline Correction and Noise Elimination, Smoothing, or JCD Algorithm.
The Mass Frontier application automatically converts a chromatogram to a matrix, where the first dimension is the scan number and the second dimension is an m/z value. Values of matrix cells are abundances. However, the oscillating m/z values of an identical ion might overlap with a different oscillating isobaric ion. In this case, it is very difficult to decide which m/z value should be taken as an independent dimension. Using the Matrix Conversion feature, you can control the alignment of oscillating m/z values to a specific value and you can visually control this process.
In the following example, the peaks are oscillating around m/z 402.15 and m/z 402.5 before matrix conversion.
Oscillating peaks on the 3D View page
In the following example, the peaks are aligned to discrete m/z 402.15 and m/z 402.5 after matrix conversion.
Aligned peaks on the 3D View page
Matrix conversion uses the Mass Merge Power parameter to determine the strength of the alignment process. The software uses this parameter also in Baseline Correction and Noise Elimination, Smoothing, and the JCD Component Detection Algorithm; however, when you calculate matrix alignment, you can watch the immediate effect on the chromatogram.
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To apply matrix conversion to your data
1.
Click the Chromatogram Processing Utilities button, , and choose Matrix.
The Matrix Conversion dialog box opens. See Matrix Conversion dialog box.
2.
3.
Click Calculate.
4.
The application returns to the Mass Merge Power value specified in Baseline Correction and Noise Elimination, Smoothing, and the JCD Component Detection Algorithm as a starting value.
5.
Matrix Conversion dialog box
Specifies the percentage of mass resolution calculated from all scans in a chromatogram. It specifies the mass difference interval within the algorithm and merges spectral peaks into one m/z value. A low value can result in more individual m/z dimensions and a high value can result in merging more ions into one.
Resets the chromatogram to its original (before matrix conversion) state. Uses the determined Mass Merge Power value in Baseline Correction and Noise Elimination, Smoothing, and the JCD Component Detection Algorithm as the starting value.
Opens the Save To Matrix Conversion Parameters File dialog box where you can save your current parameters to a Matrix Conversion parameters file (.matrix.par).
Opens the Open Matrix Conversion Parameters File dialog box where you can choose a Matrix Conversion parameters file (.matrix.par) to load.


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Related Topics:
  Fragment Ion Search (FISh)
  Force Mass Tolerance
  Thresholding
  Baseline Correction and Noise Elimination
  Smoothing
  Base Peak Chromatogram
  Background Subtraction
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