Commands:
View > Molecular References

A molecular reference view allows to define isotopic labels attached to peptides and declare within the program that isotopically labeled peptides are present in a chromatographic run. By this they influence how quantities extracted from the chromatogram are calculated and displayed. Isotopically labeled peptides are often used in a mixture with un-labeled peptides to allow precise relative quantification of many peptides and proteins.

A Molecular Reference view is generated by using the command View > Molecular References. A Molecular Reference view allows to define mass labels which are used to differentiate different sets of otherwise identical peptides in one sample. Molecular references are used for relative quantifications (see Normalization).

Activities:
  • Pressing the button adds or removes a molecular reference from the group.
  • Molecular references are based upon labelled amino acids or a labelled peptide terminus.
  • Often they consists of heavy isotopes that contain an additional number of neutrons.
  • Their additional mass can be edited directly in the added mass column.
  • For each molecular mass a colour can be defined that will be used to display associated peptide quantities in Mascot Search views or ion group views.
  • Dropping the link symbol onto a chromatogram or chromatogram map assigns the molecular references to the chromatogram. In further quantifications the chromatogram is treated as containing the molecular references as defined in the molecular references group.
  • Pressing the ⌥ key and dropping the link symbol onto a chromatogram or chromatogram map removes the molecular reference assignment from the chromatogram.