Commands:
MS/MS Chromatogram > Marker Views > Marker Group
MS/MS Chromatogram > Marker Views > Marker Group Set
File > Import > Molecular Markers...
MS/MS Chromatogram > Marker Chromatogram
MS/MS Chromatogram > Fragment Chromatogram
MS/MS Chromatogram > Unlink Molecular Markers
MS/MS Chromatogram > Modify Masses...
MS/MS Chromatogram > Show Matched Spectrum

Molecular Marker Views allow to define molecular markers for detection in a chromatogram consisting of All Ion Fragmentation data (MSE).

All Ion Fragmentation data have the characteristic that chromatograms can be generated from fragment masses since fragment spectra from all precursors within the analytical range are acquired continuously .
The main purpose of a Molecular Marker View is to relate it to an All Ion Fragmentation chromatogram to trace the marker molecules amongst all the molecules analysed. A molecular marker is considered to be detected when its m/z value and all of its fragment m/z values are detected at the same time. This is indicated by a green dot in the marker's detection column. If some of its fragment masses are not detected at the time of maximum correlation between the marker's m/z value and the fragment's m/z values the marker's detection column will show an orange dot. If there is no correlation between the marker's m/z value and it's fragments m/z values the detection column shows a red dot.

A Molecular Marker view is generated by clicking the Add View button of a Molecular Marker Group in the data collection list view or by using the command MS/MS Chromatogram > Marker Views > Marker Group. The MS/MS Chromatogram menu structure is only visible when the active view is based on a chromatographic data set generated by All Ion Fragmentation (MSE).
Molecular Marker Groups can be generated either by importing a corresponding text file via File > Import > Molecular Markers... or by calculating it from a Database Search Result or a Database Search Result Group that is correlated with its fragment spectra (see Sequences > Create Molecular Markers...).
A Molecular Marker consists of the m/z value of the intact molecule and several m/z values of fragment ions generated by the marker upon fragmentation.

Molecular Markers can be organised in sets - like peptides that belong to specific proteins. The command MS/MS Chromatogram > Marker Views > Marker Group Set generates an empty set-structured Molecular Marker Group. When calculating a marker group from a database search result the proteins assignment of peptides remains intact by generating for every protein a set. A set-structured marker group can be displayed as Marker Group Set or as conventional Marker Group using the commands MS/MS Chromatogram > Marker Views > Marker Group Set and MS/MS Chromatogram > Marker Views > Marker Group.

For overlays fragment chromatograms are individually and dynamically scaled. The order of their intensities corresponds to the acquired data. Their intensity ratios are changed for display purposes.

Activities:
  • Adding or removing Molecular Markers to / from a group: selecting the Marker table in the view and pressing the button
  • Adding or removing Fragment ions to / from a molecular marker: selecting the molecular marker, selecting the fragment ion table and pressing the button
  • Detecting the molecular marker in a chromatogram: dropping the link icon onto a chromatogram spectrum or map view
  • Detecting the molecular markers in a group of chromatograms: dropping the link icon onto a chromatogram group view
  • Clicking onto the blue intensity value of the chromatogram column of the marker table: displays the m/z chromatogram of the intact marker molecule
  • Alt-Clicking onto the blue intensity value of the chromatogram column of the marker table: displays the m/z chromatogram of the intact marker molecule and toggles the quantification method between peak fitting and area integration.
  • Clicking onto a blue value of the retention time: displays the marker molecule m/z chromatogram overlaid with all fragment m/z chromatograms
  • Clicking onto a blue m/z value in the fragment ion table: displays the marker ion m/z chromatogram overlaid with the fragment m/z chromatogram
  • Clicking onto a quantity value of a fragment displays the fragment chromatogram
  • Alt-Clicking onto a quantity value of a fragment displays the fragment chromatogram and toggles the quantification method between peak fitting and area integration.
  • A marker chromatogram from the selected molecular marker can be generated by choosing the command MS/MS Chromatogram > Marker Chromatogram
  • A fragment chromatogram from the selected fragment can be generated by choosing the command MS/MS Chromatogram > Fragment Chromatogram
  • The command MS/MS Chromatogram > Unlink Molecular Markers unlinks the molecular marker table from all chromatograms
  • The command MS/MS Chromatogram > Modify Masses... allows to modify the m/z values of all molecular markers or fragments in the selected group
  • Starting with a chromatographic peak from an intact molecule resp. a fragment ion the command MS/MS Chromatogram > Show Matched Spectrum displays a spectrum of fragment masses resp. intact ion masses which have a similar chromatographic profile (see Spectrum View)