Structure elucidation of cyclic pyoverdins and examination of rearrangement reactions in MS/MS experiments by determination of exact product ion masses

Abstract

Structure elucidation of naturally occurring linear and cyclic peptidic compounds can be complicated by rearrangement reactions induced upon collision activation (CA) when parts of the molecule migrate, suggesting incorrect substitution patterns. Such complex rearrangements are examined and discussed for two iron complexing compounds produced by the bacterial genus Pseudomonas (so-called pyoverdins). Various MS2- and MS3-product ion experiments were performed using a quadrupole-ion trap (QIT) at low resolution and a FT-ICR at high resolution allowing accurate mass determinations. The results of the multidimensional study confirm the proposed processes. On the basis of the series of tandem-MS experiments the structure of a new pyoverdin from a P. fluorescens strain [PVD(D47)] is deduced.

mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

“…b-Ions are known to lose CO to form the corresponding a-ions via the b x -a x pathway [26], which is also often described for cyclic peptides [42]–[45]. Formation of x-like ions is mechanistically possible, therefore this ion series has also been included in the software, although to the best of our knowledge these ions have not yet been described for cyclic peptides.…”

Characterization of the chromophores of pyoverdins and related siderophores by electrospray tandem mass spectrometry

“…In the following discussion, characteristic fragmentation processes for the various chromophore types will be described. Additional amino acid sequence information by MS n experiments in the ion trap (Fuchs & Budzikiewicz 2000, 2001a and possible pitfalls due to rearrangement reactions (Fuchs & Budzikiewicz 2001b;Scha¨fer et al 2006) have been discussed elsewhere. Wherever possible the characteristic processes discussed below were confirmed by comparing the fragmentation behavior of several structurally different pyoverdins and related siderophores.…”

A new 16-membered tetraene macrolide JBIR-100 from a newly identified Streptomyces species

“…However, the structure analysis of cyclic peptides, which represent an important class of bioactive natural products, by mass spectrometry, remains a challenging task. Complex fragmentation patterns by two-bond cleavage at different ring positions, ring-opening reactions and uncommon rearrangement reactions complicate the interpretation of CID-MS/MS spectra [198][199] . Frequently, higher order MS n investigations are required.…”

“…After usual working up, the oily crude extract was fractionated and purified following the scheme shown below ( Figure 111). As a result, six compounds were obtained: 4-hydroxy-10-methyl-11-oxododec-2-en-1,4-olide (236), 1,N 6 -dimethyladenosine (199), staurosporine (198), 2'-deoxy-uridine, 2'-deoxy-thymidine and 2'-deoxy-adenosine [152] . A search in AntiBase [61] resulted in two possible adenosine analogues; 1,N 6 -dimethyladenosine (199) and N,N-dimethyladenosine (200).…”

“…As a result, six compounds were obtained: 4-hydroxy-10-methyl-11-oxododec-2-en-1,4-olide (236), 1,N 6 -dimethyladenosine (199), staurosporine (198), 2'-deoxy-uridine, 2'-deoxy-thymidine and 2'-deoxy-adenosine [152] . A search in AntiBase [61] resulted in two possible adenosine analogues; 1,N 6 -dimethyladenosine (199) and N,N-dimethyladenosine (200). The experimental data are in better agreement with 199 [308,309] , however, a final decision should be made best on the basis of synthetic material: 1,N 6 -Dimethyladenosine (199) was first identified by Hammargren et al [309] as a novel nucleoside in the urine of a lung cancer patient.…”