Commands:
Sequences > Protein Group > Protein Group View
Sequences > Create Protein Group View
Sequences > Protein Group > Peptide View
Sequences > Protein Group > Unlink Peptides
Sequences > Protein Group > Create Normalization Ion Group
Sequences > Protein Group > 18O Labelling...
Sequences > Replace Amino Acids...
Sequences > Recalculate Protein Quantities
Sequences > Peptide Chromatogram
Sequences > m/z Chromatogram
Window > Residue Library
File > Export > Peptide List
File > Export > Protein Quantifications...

A protein group view is used to display and edit several proteins each one having a set of peptides. Proteins and peptides can be quantified by relating them to a chromatogram.

Protein Group views are generated by the command Sequences > Protein Group > Protein Group View or by the command Sequences > Create Protein Group View. Protein Group views are used to work with many amino acid sequences in Arcadiate. They depend on an external residue library (see command Window > Residue Library).

Protein Group View
The command Sequences > Protein Group > Protein Group View creates an empty protein group. Proteins and individual amino acid sequences can be added or deleted by using the button. Using the command Sequences > Create Protein Group View creates a populated protein group view from all the proteins and peptide sequences of a database search result.
A protein group can be viewed in two forms, grouped or ungrouped by proteins. The command Sequences > Protein Group > Peptide View displays the ungrouped form whereas the command Sequences > Protein Group > Protein Group View switches back to the protein grouped form.

Activities:
  • Associating the protein group with a chromatogram and quantifying all peptides: dropping the link icon onto a chromatogram spectrum or map view.
  • Displaying the chromatogram used for quantification: clicking on a blue coloured quantity.
  • Reassigning the protein group to a chromatogram: -link icon dropping onto a chromatogram spectrum or map view.
  • Defining a norm-protein of a chromatogram to normalise all protein quantifications to the amounts of this protein: Drag and drop a protein line onto a chromatogram, a chromatogram map or a chromatogram spectrum.
  • Displaying the quantities of proteins over several chromatograms: Drag and drop several protein lines onto a data graph view.
  • Replacing amino acid codes by other codes or inserting special N- or C- terminal codes: Sequences > Replace Amino Acids...
  • Unlinking a protein group from a chromatogram: using the command Sequences > Protein Group > Unlink Peptides.
  • Quantifying all peptides and proteins in several chromatograms: dropping the link icon onto an aligned chromatogram group view
  • Recalculating all protein quantities: using the command Sequences > Recalculate Protein Quantities.
  • Displaying the chromatogram of the first peptide isotope: selecting a peptide and using the command Sequences > m/z Chromatogram.
  • Displaying the chromatogram of significant isotopes: selecting a peptide and using the command Sequences > Peptide Chromatogram. A peptide chromatogram shows the time points where all expected isotopes of the peptide are present simultaneously. This is an improved method to detect the presence of a peptide in a mass chromatogram.
  • Peptides can be defined as being partially 18O labelled at their C-terminus. The degree of 18O labelling is set with the command Sequences > Protein Group > 18O Labelling....The labelling affects the isotopic distribution of the peptides and the way how peptide chromatograms as multiple isotope chromatograms are constructed.
  • Peptides can be unlinked from chromatograms using the command Sequences > Protein Group > Unlink Peptides.
  • Generate a Normalization Ion Group: using the command Sequences > Create Normalization Ion Group creates a normalization ion group which can be used to normalize quantities in chromatograms (see Normalization Ion Group).
  • Exporting the peptides in text format: the command File > Export > Peptide List is used to export peptides as text file.
  • Exporting the protein quantifications: in the protein groups view the command File > Export > Protein Quantifications... exports the quantified proteins in text, xml or MaxQuant Protein Groups format.