CycloBranch
Linear Siderophores

Linear Nonribosomal Peptide Siderophores

There are no special requirements for identification of desferri-forms of linear siderophores which are nonribosomal peptides (see Linear Peptides). However, the Precursor Ion Adduct must be set up for identification of ferri-forms of siderophores. The peaks of isotopes having natural abundances greater than 3% are generated automatically in theoretical peaklists next to the peaks of most abundant isotopes. If a metal is included in the precursor ion adduct field, the generated theoretical fragments are suffixed with its name and corresponding theoretical isotope fragments are generated (e.g., the fragments B4_Fe and B4_54Fe are generated instead of B4 when precursor ion adduct "FeH-2" is used).


Linear Polyketide Detail Window

The identification of linear polyketides requires an additional annotation of building blocks. See Format of Ketide Building Blocks.

The window is opened by a double-click on a row in the output report if a linear polyketide was identified. The Enter key can also be used if the row is selected. See also Linear Peptide Detail Window and Toolbar for Linear Peptides.


dfoxb.png
De novo sequencing of desferri-ferrioxamine B.


foxb.png
Sequencing of ferri-ferrioxamine B.

Nomenclature of Linear Polyketide Series

A polyketide is composed of a sequence of ketide building blocks which eliminate hydrogen atoms from both termini or eliminate a molecule of water. A linear polyketide can have N-terminus and C-terminus; but also two N-termini or two C-termini. CycloBranch generates 8 basic series of fragment ions for linear polyketides (L and R stand for left and right, respectively):

  • Lb (left b-ion)
  • Lb + 2H (left b-ion + 2H)
  • Rb (right b-ion)
  • Rb + 2H (right b-ion + 2H)
  • Ly (left y-ion)
  • Ly - 2H (left y-ion - 2H)
  • Ry (right y-ion)
  • Ry - 2H (right y-ion - 2H)

7 additional series of fragment ions are followed for each of the basic series:

  • CO loss
  • H2O loss
  • NH3 loss
  • H2O + NH3 loss
  • CO + H2O loss
  • CO + NH3 loss
  • CO + H2O + NH3 loss

In total, 64 series of fragment ions are defined for linear polyketides:

  • LB
  • LB* (H2O loss)
  • LBx (NH3 loss)
  • LB*x (H2O + NH3 loss)
  • LB-CO
  • LB*-CO
  • LBx-CO
  • LB*x-CO
  • LB+2H
  • LB*+2H
  • LBx+2H
  • LB*x+2H
  • LB+2H-CO
  • LB*+2H-CO
  • LBx+2H-CO
  • LB*x+2H-CO
  • RB
  • RB*
  • RBx
  • RB*x
  • RB-CO
  • RB*-CO
  • RBx-CO
  • RB*x-CO
  • RB+2H
  • RB*+2H
  • RBx+2H
  • RB*x+2H
  • RB+2H-CO
  • RB*+2H-CO
  • RBx+2H-CO
  • RB*x+2H-CO
  • LY-2H
  • LY*-2H
  • LYx-2H
  • LY*x-2H
  • LY-2H-CO
  • LY*-2H-CO
  • LYx-2H-CO
  • LY*x-2H-CO
  • LY
  • LY*
  • LYx
  • LY*x
  • LY-CO
  • LY*-CO
  • LYx-CO
  • LY*x-CO
  • RY-2H
  • RY*-2H
  • RYx-2H
  • RY*x-2H
  • RY-2H-CO
  • RY*-2H-CO
  • RYx-2H-CO
  • RY*x-2H-CO
  • RY
  • RY*
  • RYx
  • RY*x
  • RY-CO
  • RY*-CO
  • RYx-CO
  • RY*x-CO

If a metal is included in the precursor ion adduct field, the generated theoretical fragments are suffixed with its name and corresponding theoretical isotope fragments are generated (e.g., the fragments LB3+2H_Fe and LB3+2H_54Fe are generated instead of LB3+2H when precursor ion adduct "FeH-2" is used). See also Precursor Ion Adduct. A mass spectrometry nomenclature for linear polyketide siderophores is shown in the following figure.

linearketideseries.png
Mass spectrometry nomenclature for linear polyketide siderophores; ketide building blocks - Hpd (N-Hydroxy-1,5-pentanediamine; a) and Suc (Succinic semialdehyde; b); fragment ion series of desferrioxamine B (c), and desferrioxamine G1 (d).

Linear Polyketide Sequence Detection

The detection of linear polyketide sequence candidates is similar to the detection of linear peptide sequence candidates. See Linear Sequence Detection.

A difference is that four starting points are applicable to linear polyketides: H+, H+ + 2H, H3O+ and H3O+ - 2H. If a ferri-form of a siderophore is being detected, masses of all starting points must be increased by mass of Fe - 3H. The process is analogous for other metals.