Retention time alignment is based on finding common peptide landmarks between two files, selecting one file is the reference file and correcting the retention times for the other file to be as close as possible to the reference file for all peptides. As input for the regression, the application uses only those landmarks found in both files.

The result file must contain label-free quantification results for the File Alignment view to be available.

Procedure

  1. In the result file, select the Input Files tab (use the Result Table Chooser to make it visible if necessary).
  2. The Input Files page displays the input data for the regression and the calculated correction curve.
  3. Each file is aligned to one reference file.
  4. Select an input file.
  5. Select View > File Alignment View.
  6. The File Alignment view opens.
  7. File Alignment view

The File Alignment view displays how the selected file is aligned to its reference file. The reference file is shown in the Ref. File ID column of Input Files page and in the legend of the correction plots.

  • The x-axis value used for the regression is the retention time of the identified peptides in the reference file.
  • The y-axis value is the retention time difference between the landmarks.