Commands:
Sequences > Database Group View
Sequences > Database Group Peptide View
Sequences > Unlink Fragment Spectra...
File > Export > Peptides...
File > Export > Protein Quantifications...
Sequences > Create Protein Group View
Sequences > Create Molecular Markers...
Sequences > Replace Amino Acids...
Sequences > Reset Determ. Retention Times and MZs
Sequences > Recalculate Protein Quantities
Sequences > Peptide Chromatogram
Sequences > m/z Chromatogram
Sequences > Unlink Fragment SpectraEdit > Cut
A database search group allows to combine several database searches. Proteins and peptides are not merely copied but combined such that duplicate peptides and proteins are avoided. Database search groups can be edited. They are used to quantify proteins based on all peptides found in several different chromatographic runs.
A Database Search Group view is generated by using the command Sequences > Database Group View. The Database Search Group view displays all the proteins and peptides of the database search results in its group. When adding a database search result peptide sequencing belonging to a protein already present in the group are added without duplicating the protein entry. All the peptides can be displayed as a list by using the command Sequences > Database Group Peptide View or ordered by proteins via the command Sequences > Database Group View.
Activities:
- Associating fragment spectra with peptide sequences: dropping the link icon
onto a chromatogram group view
- Displaying the fragment spectrum with its peptide sequence: clicking on a blue coloured amino acid sequence
- Removing an association between a database search and the fragment spectra: command Sequences > Unlink Fragment Spectra...
- Determining the ion volume of the first isotope of identified peptides in a chromatogram: dropping the link icon
onto a chromatogram group view
- Displaying the noise reduced chromatogram of the first isotope of an identified peptide: clicking on a blue coloured ion volume figure
- Editing the precursor ion volume: displaying its chromatogram and changing its selection by ⌘ click-dragging over the chromatogram
- Re-establishing the default ion volume figure: clicking on a blue coloured ion volume figure of the peptide
- Determining the first isotope ion volumes of identified precursors in several chromatograms: dropping the link icon
onto a chromatogram group whose chromatograms are aligned.
- 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.
- Exporting peptides: the command File > Export > Peptides... exports all peptides as a tab separated list
- Exporting quantification results: the command File > Export > Protein Quantifications... allows to export the ion volumes and sequences of all selected proteins in a structured way as a tab separated list
- Creating a protein group whose sequences can be edited: Sequences > Create Protein Group View.
- Creating a molecular marker group: The command Sequences > Create Molecular Markers... creates a molecular marker group from peptides which are linked to their fragment spectra.
- Sequences > Replace Amino Acids... allows to replace all occurrences of specific amino acids by for instance modified amino acids
- The command Sequences > Reset Determ. Retention Times and MZs resets the retention times and m/z values of peptides as they were determined when associating them with fragment spectra to the original retention times and m/z values as they were recorded in the database search results.
- With Sequences > Recalculate Protein Quantities all protein quantities are recalculated in accordance with the actual settings (see Arcadiate > Preferences > Quantification and the different normalisation settings).
- The command Sequences > Peptide Chromatogram displays a peptide chromatogram of the currently selected peptide. A peptide chromatogram can consider several isotopes.
- Sequences > m/z Chromatogram displays the chromatogram of the first isotope of the selected peptide.
- Sequences > Unlink Fragment Spectra unlinks the peptides from their fragment spectra.
- Database search group views are editable - with Edit > Cut the selected proteins, selected peptides or the view itself can be deleted.