CycloBranch
Cyclic Siderophores

Cyclic Nonribosomal Peptide Siderophores

There are no special requirements for identification of desferri-forms of cyclic siderophores which are nonribosomal peptides (see Cyclic Peptides). The precursor ion adduct must be set up for identification of their ferri-forms (see Linear Nonribosomal Peptide Siderophores).


Cyclic Polyketide Detail Window

The identification of cyclic 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 cyclic polyketide was identified. The Enter key can also be used if the row is selected. See also Cyclic Peptide Detail Window and Toolbar for Cyclic Peptides.


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De novo sequencing of desferri-ferrioxamine E.


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De novo sequencing of ferri-ferrioxamine E.

Nomenclature of Cyclic Polyketide Series

The nomenclature of cyclic polyketides is based on the nomenclatures of linear polyketides and cyclic peptides. See Nomenclature of Linear Polyketide Series and Nomenclature of Cyclic Series. CycloBranch generates 2 basic series of fragment ions for cyclic polyketides (L and R stand for left and right, respectively):

  • Lb (left b-ion)
  • Lb + 2H (left b-ion + 2H)

Rb and Rb + 2H series series are not generated because the fragment ions are redundant with the series Lb and Lb + 2H. The fragment ion series Ly, Ly - 2H, Ry and Ry - 2H (utilized in Nomenclature of Linear Polyketide Series) are not applicable to cyclic polyketide siderophores due to head-to-tail cyclization.

Like in the case of cyclic peptides, CycloBranch generates theoretical series of ions i-j,Lb and i-j,Lb + 2H where i-j are numbers of building blocks between which a ring having n building blocks is opened (i,j <= n; i=1, j=n; or i=j+1, otherwise). CycloBranch also generates reversed series of ions j-i,Lb and j-i,Lb + 2H.

When 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 cyclic polyketide siderophore desferrioxamine E is shown in the following figure.

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Mass spectrometry nomenclature for cyclic polyketide siderophore desferrioxamine E.

Cyclic Polyketide Sequence Detection

The detection of cyclic polyketide sequence candidates is based on Linear Polyketide Sequence Detection and Cyclic Sequence Detection. The starting points applicable to cyclic polyketides are H+ and H+ + 2H.


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De novo graph created from the experimental spectrum of ferrioxamine E (Hpd = N-Hydroxy-1,5-pentanediamine; Suc = Succinic semialdehyde).