The Precursor Isotope Pattern view displays the m/z range of the corresponding master scan from which the fragmented precursor ion was extracted. It shows the isotope pattern of the precursor ion associated with the identified PSM. You can use this view to assess the abundance and intensity of the precursor ion or to reference the experimentally determined mass of the precursor ion and its isotopes, the isolation window, or other details.

You can display the Precursor Isotope Pattern view for each MS2 spectrum and for each PSM.

To preserve storage space, the application does not store the full master scan but only the peaks from a small mass range around the precursor mass. This arrangement provides a large enough range so that you can see both the full width of the isolation window used and the full isotope pattern of the precursor. The default mass range is from 2.5 Da below the lower boundary of the isolation window to 5.5 Da above the upper boundary of the isolation window.

If you do not want to use these default settings, you can use the following two parameters of the Spectrum Selector node to change them:

  • The Precursor Clipping Range Before parameter, which specifies the lower limit below the isolation window of the mass range from which to extract peaks for the Precursor Isotope Pattern view.
  • The Precursor Clipping Range After parameter, which specifies the upper limit above the isolation window of the mass range of from which to extract peaks for the view.

For example, if the precursor m/z is 1,000 and the isolation window is 4 Da, you would extract peaks from the master scan starting at:

(precursor_m/z – half_the_isolation_window – Precursor_Clipping_Range_Before_setting)

up to:

(precursor_m/z + half_the_isolation_window + Precursor_Clipping_Range_After_setting).

In numeric terms, this equation is (1000 – 2 – 2.5) = 995.5 to (1000 + 2 + 5.5) = 1007.5.

For more information on the Precursor Clipping Range Before parameter and the Precursor Clipping Range After parameter, see the Spectrum Selector node in the Proteome Discoverer Help.

Procedure

  1. In an open report, select the PSMs tab or select a peptide beneath a protein on the Proteins page.
  2. Select the appropriate peptide row.
  3. Select View > Precursor Isotope Pattern, or select Precursor Isotope Pattern .
  4. The mass spectrum of the precursor ion opens.
  5. Precursor Isotope Pattern view

This view has the following features:

  • The yellow region displays the isolation width of the instrument, which is the portion of an MS scan that was further subjected to an MS/MS scan.
  • A red line indicates the monoisotopic precursor mass-to-charge ratio (m/z) determined by the instrument during acquisition.
  • A blue line marks the calculated monoisotopic precursor mass and represents the reevaluated monoisotopic mass-to-charge ratio (m/z) value for the detected peptide.
  • A green line indicates the selected monoisotopic mass.

Use the Precursor Isotope Pattern view to verify that the correct monoisotopic mass has been calculated, because the first isotope of a peptide might not be the most intense ion. For example, the blue line represents the monoisotopic mass that the application calculated, and the red line represents the monoisotopic mass that the mass spectrometer calculated. When the spectrometer selects the correct monoisotopic mass, these two lines should line up. However, the two lines are divergent, indicating that the mass spectrometer picked the wrong monoisotopic mass.