You can run an Intact Mass Analysis experiment in Automatic or Manual mode:

  • In Automatic mode, the application automatically processes your experiment using the parameters in the selected processing method.
  • In Manual mode, you can determine the optimal settings for selecting chromatographic peaks and deconvolving the spectrum before processing your experiment. After you determine the optimal settings, you can save them to a processing method which will be available for use in Automatic mode for subsequent experiments.

IMPORTANT

The Batch Processing results format is not supported for Intact Mass Analysis experiments processed in Manual mode.

You must select the Multiconsensus results format to process an Intact Mass Analysis in Manual mode.

IMPORTANT

The Auto Peak Detection deconvolution method is not supported for Intact Mass Analysis experiments processed in Manual mode.

You must select a processing method using the Average Over Selected Retention Time or Sliding Windows deconvolution method to process an Intact Mass Analysis in Manual mode.

Comparison of Manual and Automatic modes for Intact Mass Analysis

Manual mode

Automatic mode

Steps

In Manual mode, you must manually perform the following:

  1. Set up the chromatogram
  2. Select the chromatographic peaks
  3. Edit the algorithm parameters to deconvolve the spectra
  4. Review and report experiment results

In Automatic mode, the application automatically performs the following:

  1. Detects chromatographic peaks
  2. Extracts averaged mass spectra
  3. Deconvolves isotopically unresolved or resolved data
  4. Generates a list of components

Results format

  • Multiconsensus
  • Batch Processing
  • Multiconsensus

Deconvolution algorithm

  • Xtract
  • ReSpect
  • Xtract
  • ReSpect

Deconvolution methods

  • Average Over Selected Retention Time
  • Sliding Windows
  • Average Over Selected Retention Time
  • Auto Peak Detection
  • Sliding Windows

Action on the Intact Mass Analysis page

Select the Manual Process button to open the Process and Review page and manually specify experiment settings.

Select the Add to Queue button to add the experiment to the run queue for processing.