CycloBranch
Linear Peptides

Linear Peptide Detail Window

The window is opened by a double-click on a row in the output report if a linear peptide was identified. The Enter key can also be used if the row is selected. The title of the window contains a "Result ID" of a peptide sequence candidate.

lineardetail.png
De novo sequencing of gramicidin C.

A graphical visualization of the experimental spectrum is shown on the left at the top. Experimental peaks matched with theoretical peaks are red. A graphical visualization of a peptide sequence is shown on the right at the top.

A list of theoretical peaks is shown in the table on the left at the bottom. Following details are available:

  • Fragment Type - a name of a theoretical peak including information about its charge
  • Theoretical m/z - a theoretical mass-to-charge ratio of the peak
  • Experimental m/z - a mass-to-charge ratio of a matched peak
  • Relative Intensity [%] - a relative intensity of a matched peak
  • Absolute Intensity - an absolute intensity of a matched peak
  • Error [ppm] - a ppm error
  • Sequence - a sequence of building blocks corresponding to the peak

The theoretical peaks assigned to experimental peaks are red. A list of unassigned experimental peaks is at the bottom of the table. The only items reported for unassigned experimental peaks are "Experimental m/z", "Relative Intensity [%]", and "Absolute intensity".

Following additional details are shown in a text window on the right at the bottom:

  • Acronym Peptide Name - a name of the peptide sequence candidate composed from acronyms of building blocks; you can click on an acronym to see the details in ChemSpider, PubChem, etc.
  • Full Peptide Name - a name of the peptide sequence candidate composed from full names of building blocks.
  • Path in the De Novo Graph - you can see details about a path in the de novo graph from which the peptide sequence candidate was determined.
  • Series of matched peaks - the series of matched peaks are shown for each fragment ion type defined in Ion Types in Theoretical Spectra. For each series, a vector of integers is shown, e.g., "B 0 0 1 1 1 1 1 1 1 1 0 0 0 0" means that a consecutive series of ions b3-b10 was matched. 0 means that a theoretical fragment ion was not matched. A value greater than '1' can be shown when multiple charge variants of the same theoretical peak were matched.

Toolbar for Linear Peptides

Export Table to CSV (CTRL + E)

Export the table of peaks into a csv (comma separated values) file.

Export Image (CTRL + G)

Export the spectrum/peptide image into a PDF, PS (Windows only), PNG or SVG file. PS files in Linux can be generated outside of the application, e.g., using the pdf2ps tool.

Find Text (CTRL + F)

A find text dialog is opened.

Find Previous (CTRL + 1)

Move the cursor to the previous search result when a text was found.

Find Next (CTRL + 2)

Move the cursor to the next search result when a text was found.

Zoom In (CTRL +; mouse wheel up)

The window with the graphical visualization of an experimental mass spectrum on the left at the top is zoomed in. A zoom factor in the range <1, 32> is increased by 0.2 when the button is pressed.

Zoom Out (CTRL -; mouse wheel down)

The window with the graphical visualization of an experimental mass spectrum is zoomed out. The zoom factor is decreased by 0.2 when the button is pressed.

Zoom Reset (CTRL + R)

The zoom factor is set up to 1 when the button is pressed.

Absolute Intensity (CTRL + I)

View absolute/relative intensities of peaks.

Hide Matched Peaks (CTRL + M)

All experimental peaks which are red (i.e., they have been assigned to theoretical peaks) are hidden in the graphical visualization of an experimental mass spectrum on the left at the top if the button is checked. If the button is unchecked, the peaks are visible. The red peaks in the peaks table are also hidden if the button is checked.

Hide Unmatched Peaks (CTRL + U)

All experimental peaks which were not assigned to theoretical peaks are hidden if the button is checked. If the button is unchecked, the peaks are visible. The unmatched theoretical and experimental peaks in the peaks table are also hidden if the button is checked.

Mouse m/z Selection Tool (CTRL + T)

If the button is enabled, the mouse can be used to select a range of m/z ratios to be shown.

  • Left mouse button - press and hold the button to draw a rectangle determining the minimum and maximum values of m/z ratios; release the button to apply the changes.
  • Right mouse button - press the button during the drawing of a rectangle to cancel the drawing.
  • Middle mouse button - reset the range of m/z ratios.

m/z

  • First field - a minimum value of m/z ratio to be shown.
  • Second field - a maximum value of m/z ratio to be shown.
  • "Set" button (or Enter key) - apply the changes.
  • "Reset" button - reset the range of m/z ratios.

Linear Sequence Detection

A path in a de novo graph corresponding to a linear peptide sequence is detected as shown in the following scheme, i.e, from H+ to precursor ion for b-series or from H3O+ to precursor for y-series. An edge corresponds to a residue mass of a building block or to a sum of residue masses of a combination of building blocks. If an edge corresponds to multiple building blocks, peptide sequence candidates with all permutations of building blocks are generated from a path in a de novo graph. For example, if the edge corresponds to a combination of blocks leucine, proline and valine, the order of blocks can be LPV, LVP, PVL, PLV, VLP, and VPL; and thus 6 peptide sequence candidates are generated.

linear-denovo.png
Detection of a path corresponding to a linear peptide in a de novo graph.