CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

Novák, Jiří; Lemr, Karel; Schug, Kevin A.; Havlı́ček, Vladimı́r

doi:10.1007/s13361-015-1211-1

Cited by 36 publications

(45 citation statements)

References 28 publications

(29 reference statements)

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“…Two of the most recent algorithms are CYCLONE and CycloBranch, which were developed to characterize cyclic peptides via a de novo strategy [48,49]. An in-house algorithm was developed in C# to assign fragment ions of cyclic peptides based on interpretation of 193 nm UVPD mass spectra.…”

Section: Development Of a Custom Algorithm For Assignment Of Fragmentmentioning

confidence: 99%

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

Crittenden

Parker

Jenner

et al. 2016

J. Am. Soc. Mass Spectrom.

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Abstract. A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the aminecontaining portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.

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Section: Development Of a Custom Algorithm For Assignment Of Fragmentmentioning

confidence: 99%

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

Crittenden

Parker

Jenner

et al. 2016

J. Am. Soc. Mass Spectrom.

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“…The database approach does not require the verification of the molecular formula because it presumes that the correct formula is available in the database. This database approach is also supported by DataAnalysis, mMass, and our in‐house software CycloBranch …”

Section: Introductionmentioning

confidence: 99%

“…Product ion mass spectra of natural products can be searched against databases (eg, GNPS) or compared to fragmentation mass spectra generated in silico . If the compound structure has not been observed previously, its experimental spectrum can also be probed via de novo sequencing . A common drawback of the current free tools is the lack of support of the fine isotope patterns, both in conventional and product ion mass spectra …”

Section: Introductionmentioning

confidence: 99%

“…This database approach is also supported by DataAnalysis, mMass, and our in-house software CycloBranch. 6,7 Algorithms for the prediction of theoretical isotope patterns from molecular formulas have recently been reported. 8 Many of these algorithms are optimized for low-resolution data, in part because the mathematical calculation of a complete isotope pattern is time consuming.…”

mentioning

confidence: 99%

“…3,14,15 If the compound structure has not been observed previously, its experimental spectrum can also be probed via de novo sequencing. 6 A common drawback of the current free tools is the lack of support of the fine isotope patterns, both in conventional and product ion mass spectra. 16 Pyoverdines are a large family of nonribosomal peptides and siderophores (ie, iron-chelating compounds) produced by pseudomonads.…”

mentioning

confidence: 99%

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CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra

et al. 2018

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Within the growing community of Fourier transform mass spectrometry users, the identification of fine isotope structure has become an indispensable method for molecular formula determination. In this work, the fine isotope envelopes for accessing the mutual ratio of 2 closely related pyoverdines in a mixture were used. Bacterial siderophores pyoverdines D and E cannot be easily separated via liquid chromatography-mass spectrometry because their structures differ in (de)amidation at the respective chromophore parts only. Their mutual ratio was determined in a mixture via nuclear magnetic resonance spectroscopy and semiquantitative mass spectrometry using our open-source software CycloBranch, which represents a genuine free tool supporting the determination of fine isotope structures in both conventional and product ion mass spectra. Native Bruker, Thermo, and Waters data formats are supported in addition to XML and plain text formats.

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Aspergillus infection monitored by multimodal imaging in a rat model

et al. 2016

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Although myriads of experimental approaches have been published in the field of fungal infection diagnostics, interestingly, in 21st century there is no satisfactory early noninvasive tool for Aspergillus diagnostics with good sensitivity and specificity. In this work, we for the first time described the fungal burden in rat lungs by multimodal imaging approach. The Aspergillus infection was monitored by positron emission tomography and light microscopy employing modified Grocott's methenamine silver staining and eosin counterstaining. Laser ablation inductively coupled plasma mass spectrometry imaging has revealed a dramatic iron increase in fungi-affected areas, which can be presumably attributed to microbial siderophores. Quantitative elemental data were inferred from matrix-matched standards prepared from rat lungs. The iron, silver, and gold MS images collected with variable laser foci revealed that particularly silver or gold can be used as excellent elements useful for sensitively tracking the Aspergillus infection. The limit of detection was determined for both (107) Ag and (197) Au as 0.03 μg/g (5 μm laser focus). The selective incorporation of (107) Ag and (197) Au into fungal cell bodies and low background noise from both elements were confirmed by energy dispersive X-ray scattering utilizing the submicron lateral resolving power of scanning electron microscopy. The low limits of detection and quantitation of both gold and silver make ICP-MS imaging monitoring a viable alternative to standard optical evaluation used in current clinical settings.

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CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

Cited by 36 publications

References 28 publications

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra

Aspergillus infection monitored by multimodal imaging in a rat model

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