CycloBranch
Branched Peptides

Branched Peptide Detail Window

The window is opened by a double-click on a row in the output report if a branched peptide was identified. The Enter key can also be used if the row is selected.

brancheddetail.png
De novo sequencing of linearized pseudacyclin A.

See also Linear Peptide Detail Window. The differences for branched peptides are following:

  • The text window on the right at the bottom contains a list of all six linearized sequences derived from a singly branched peptide sequence.
  • A name of a fragment ion is prefixed with a number of a linearized sequence from which the fragment ion was generated (e.g., 2_B1 means that the fragment ion b1 was generated from the linearized sequence no. 2).

Numbers of linearized sequences of a branched peptide sequence are defined as follows (with respect to the visualization of a branched peptide):

  • sequence no. 1 - starts on the left, ends on the right;
  • sequence no. 2 - starts at the top, ends on the right;
  • sequence no. 3 - starts on the right, ends on the left;
  • sequence no. 4 - starts on the left, ends at the top;
  • sequence no. 5 - starts at the top, ends on the left;
  • sequence no. 6 - starts on the right, ends at the top.

The start point of a linearized sequence corresponds to a theoretical N-terminus. The end point corresponds to a theoretical C-terminus.


Toolbar for Branched Peptides

See also Toolbar for Linear Peptides. The differences for branched peptides are following:

Linearized sequence

A dropdown menu is shown where you can choose which peaks are red in the spectrum of the left and which fragment ions are shown in the visualization of a branched peptide on the right. You can choose that only theoretical peaks from one linearized sequence (e.g., 2) are red if they were matched with experimental peaks. In this case, the visualization of the peptide on the right shows only matched fragment ions from the linearized sequence 2. The default value "all" means that all matched theoretical peaks are red in the spectrum on the left and that all matched fragment ions are shown in the visualization of the peptide on the right.


Branched Sequence Detection

Series of fragment ions of a branched peptide are shown in the following picture.

branched-series.png
Theoretical fragmentation of a branched peptide.


A path in the de novo graph corresponding to a branched peptide is detected as is shown in the following scheme (an edge corresponds to a residue mass of a building block or a sum of residue masses of a combination of building blocks). An edge corresponding to the branch must include at least two building blocks (one block cannot form a branch).

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


Since peaks determining the begin and the end of a branch may be missing in an experimental spectrum, the algorithm generates a set of peptide sequence candidates from a path in the graph instead of one sequence candidate. See the following scheme.

branched-detection.png
Peptide sequence candidates generated from a path in a de novo graph (branched peptides).



Nomenclature of Branched Series

In the following picture, you can see a general scheme of a fragmentation of a singly branched peptide. A sequence of a branched peptide can be written by six different ways (called linearized sequences of a branched peptide sequence). Two series of ions can be generated from each linearized sequence (N-terminal and C-terminal), thus we get series of fragment ions 1B to 6B and 1Y to 6Y. However, the series 3B, 5B and 6B are unsense because N-terminal fragments cannot be generated from a C-terminal side. Similarly, the series 3Y, 5Y and 6Y are unsense because C-terminal fragments cannot be generated from an N-terminal side. The series 2B and 2Y exist only when the branch is N-terminal. The series 4B and 4Y exist only when the branch is C-terminal. Thus for a branched peptide, only four series of fragment ions can be observed in total - two series of b-ions (N-terminal ions) and two series of y-ions (C-terminal ions).

tpeptidefragmentation.png
General scheme of a fragmentation of a branched peptide.

Fragmentation Example

A scheme of theoretical fragments generated from a linearized pseudacyclin A is shown in the following picture. We assume that a ion of a branched peptide is fragmented only once and that the branch is not fragmented, thus some b-ions and y-ions do not exist in the theoretical spectrum (struck out in the following picture). If a branch was split, the ion would be fragmented for second time.

tpeptidefragmentation-v2-nocolor.png
Theoretical fragments of linearized pseudacyclin A and its six linearized sequences (P = proline; I = isoleucine, Or = ornithine; aI = acetylisoleucine; F = phenylalanine).


pseudacyclin-linearized.png
Linearized pseudacyclin A.

Branched Siderophores

CycloBranch supports the identification of desferri- and ferri-forms of branched siderophores which are nonribosomal peptides. For details, see Linear Nonribosomal Peptide Siderophores.