Christie Hunter


How do I check the quality of the Auto Retention Time Calibration used in my Extractor processing?

When using the Auto-Calibration option in Extractor, a set of retention time calibration peptides will be determined automatically from the library and used for RT calibration.

To determine how the fit looks for the calibration on each datafile, follow these steps.

  • Browse to the folder or project that contains the Extractor analysis for your experiment (in SCIEX Cloud or BaseSpace)
  • Find the “_calibrate_<sample>” and download to your computer
  • Rename the file to *.zip and unzip the file
  • Find the ForwardPeptideResults.txt and open this in Excel
  • First sort the data by descending Score.
  • Compute the median value for all the score values in this column
  • Next plot Library RT vs. Observed RT using only the rows with scores above the median score value. These are the peptides that were used for RT calibration. Add a linear trendline to the plot and show the equation and R-squared on the plot
  • This provides a visual of the peptides used and the linear fit

Note that this provides an approximation of the fit if there are outliers present.


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