Commands:
Arcadiate > Preferences...

Use the command Arcadiate > Preferences... to access the preference settings.

Spectrum
  • Color of Spectrum
  • Color of Chromatogram
  • Color of Overlay: an overlay is generated by dropping a spectrum onto another spectrum view using the view icon
  • Color of MS/MS Chromatogram: color of a chromatogram generated from fragment ions - applicable for All Ion Fragmentation (MSE) data
  • Automatic and manual peak labelling
  • Expanding centroided data: centroided data is displayed in profile mode
  • Lowest expanded peak intensity: this value influences centroiding procedures. Only peaks whose expanded peak intensity is beyond this value will be retained when centroiding the data
  • Chromatographic m/z broadening: This factor affects the m/z range of automatically generated chromatograms. The range proposed from the measured spectrum characteristics is multiplied by this factor.

Quantification
  • Quantify within Chromatograms: by peak matching or by integration - peak matching means that the elution profile is matched against a characteristic peak form. The matched peak is integrated. This quantification method can be more robust against overlapping chromatographic peaks. It is the default option. By Integration means that the intensity profile itself is integrated.
  • Molecular Reference Quantity: Molecular reference are labeled molecules whose intensity serve as normalization for the quantity of the actually measured molecule
    • Determination: by chromatographic peak comparison - the intensity of both the reference molecule and the measured molecule are determined by integrating their resp. ion chromatogram. The ratio between the two integrals is the actual result
    • Determination: by spectral peak comparison - the intensity of the reference molecule and the measured molecule are measured both within the same spectra. The ratios between the peak intensities are averaged and is the actual result. This mode requires that molecular reference and measured molecule have the same retention time. If this is the case this method is more robust than the chromatographic peak comparison
    • Display: relative or absolute - the intensity of the measured molecule can be displayed as a relative value to its molecular reference or as an absolute value.
  • Peptide Chromatogram:
    • constructed using only the first isotope
    • constructed using several isotopes - this option requires the presence of all considered isotopes to yield a chromatographic intensity.
  • Protein Quantity Calculation: Protein quantities are calculated from their peptide quantities. The average of the three most abundant peptides reflects that the digesting enzyme does not digest proteins in a homogeneous way. Only the most abundant peptides might reflect the chemical concentration of the protein. Calculating the protein quantity as the sum of all peptides divided by the protein mass is statistically a more robust value and the default choice when relative protein changes between experiments is the important observation.
  • Time resolution of Chromatogram Normalizations: This parameter controls the density of normalisation points when normalising chromatograms to reference molecules. The default value is 10 minutes.
  • Normalise Chromatograms by their Total Ion Count: This parameter declares whether two chromatograms should be normalised so that they have the same total ion count. This is often use to compensate for differences in the total amount of material used for mass spectrometric runs.
  • Display Normalized Protein Quantities: Decides whether protein quantities in Database Search Result views are displayed as relative values, normalized to the quantities of a norm-protein defined by dropping a protein-line from a Database Search View onto a chromatogram map or spectrum.

Miscellaneous
  • Width of Chromatogram for Display: this parameter limits the reconstruction of chromatograms to this time window. 0 means that chromatograms will be reconstructed over the complete time range.
  • Insert Modified Amino Acid Code when Importing Sequences: Database search engines can determine whether some amino acids in the identified peptide were modified. They often can not specify their location. If this option is chosen and the import detects that a peptide sequence is modified it replaces the first occurrence of the unmodified amino acid code by its modified amino acid code. The detection of a specific modification is based on descriptors associated with the modified amino acid in the residue library.
  • Display Tool Tips: toggles the on-screen display of tool tips
  • Reset Dialogs: some dialogs offer the possibility not to show them any longer. Pressing this button tells all these dialogs to reappear.