The following table describes the parameters in the Chromatogram Parameters area on the Component Detection page.

Chromatogram Parameters area on the Component Detection page

Parameter

Description

Use Restricted Time (checkbox)

Select to zoom the part of the chromatogram that you define with the Time Limits/Scan Range parameters.

When cleared (default), the application displays the entire chromatogram.

Time Limits

(Enabled only when you select the Use Restricted Time checkbox and a chromatogram is visible in the Chromatogram pane) Specifies the beginning and end retention time (RT) range of the chromatogram that you want to view.

The default values for both limits depend on the data in the raw data file.

The values that you enter link to the values that appear in the Scan Range boxes and update both sets of parameters.

Scan Range

(Enabled only when you select the Use Restricted Time checkbox and a chromatogram is visible in the Chromatogram pane) Specifies the beginning and end scans of the range of the chromatogram that you want to view.

The default values for both limits depend on the data in the raw data file.

The values that you enter link to the values that appear in the Time Limits boxes and update both sets of parameters.

m/z Range

Specifies the range of m/z values used as input to the deconvolution. The deconvolution algorithm ignores the portions of the spectrum outside this range.

Intact proteins typically show up at a higher m/z values and small molecule contaminants and background noise fall below 600m/z. Therefore, you might choose to narrow the m/z range.

Exercise caution in specifying the width of the m/z range. Using an m/z range that is too large might cause the deconvolution algorithm to incorporate weak, noisy, and poorly characterized peaks into some of its fittings, with a corresponding loss in the quality of the results. In general, try to restrict the m/z range to the most intense regions of the spectrum.

Chromatogram Trace Type

Determines the type of chromatogram displayed in the Chromatogram pane: TIC (total ion chromatogram) or BPC (base peak chromatogram).

Sensitivity

Specifies the sensitivity with which the chromatographic peak detector identifies peaks.

  • Low: Directs the chromatographic peak detector to perform one pass at the default sensitivity.
  • High: Directs the chromatographic peak detector to perform a second pass at higher sensitivity−that is, with a slightly narrower width threshold−to identify narrow shoulders or noise-like peaks that the peak detector might have missed in the first pass.
  • This option increases peak sensitivity but also the potential false-positive rate.

Rel. Intensity Threshold (%)

Sets an intensity threshold for peaks in the chromatogram, as a percentage. The application ignores peaks with relative intensities below this threshold.

This parameter is different from the Rel. Abundance Threshold (%) (Xtract) or Rel. Abundance Threshold (%) (ReSpect) parameter, which sets a lower intensity for signals in the spectrum, not in the chromatogram.