Commands:
Sequences > Database Protein View
Sequences > Database Peptide View
Sequences > Create Protein Group View
Sequences > Unlink Fragment Spectra...
File > Export > Peptides...
File > Export > Protein Quantifications...
File > Export > Database Search Result as xml...
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 Spectra
A database search view displays the identified proteins each with its set of identified peptides. They are used for quantifying identified proteins.
A Database Search Result view is generated by clicking its Add View button in the data collection list view. The Database Search Result view displays all the identified proteins and their associated peptide sequences. A Database Search can be displayed with the peptides grouped by protein with the command Sequences > Database Protein View or as a list of all peptides with the command Sequences > Database Peptide View.
Activities:
- Associating fragment spectra with peptide sequences: dropping the link icon
onto a chromatogram 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 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. The database search has to be linked with a chromatogram that is part of the group to define the retention times of the precursors in the other chromatograms.
- 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
- Exporting the Database Search Result in Mascot XML format: File > Export > Database Search Result as xml...
- Accessing the URL of the original Database Search Result: clicking the URL-button
- Editing the URL of the original Database Search Result: ⌥-clicking the URL-button
- 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.