Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra

Baumgaertel, Anja; Scheubert, Kerstin; Pietsch, Bernhard; Kempe, Kristian; Crecelius, Anna C.; Böcker, Sebastian; Schubert, Ulrich S.

doi:10.1002/rcm.5019

Cited by 13 publications

(13 citation statements)

References 24 publications

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“…The proteomics field has benefited tremendously from this development; often only the use of these automated methods enables high-throughput proteomics experiments. Computational methods for the analysis of proteins and peptides, as well as DNA and RNA [22,23], glycans [24-26], or synthetic polymers [27,28] are also part of computational mass spectrometry, but outside the scope of this review. Finally, disclosing methods is important for reproducible science.…”

Section: Introductionmentioning

confidence: 99%

Computational mass spectrometry for small molecules

2013

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The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline.

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Section: Introductionmentioning

confidence: 99%

Computational mass spectrometry for small molecules

2013

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“…In this contribution, other than the application of tandem mass analysis of CRP‐generated polymers via various ionization techniques for investigating the differences in fragmentation patterns, we would like to present the automated evaluation of tandem mass spectra of homopolymers by utilizing the PLUMS software for a faster and easier analysis (http://bio.informatik.uni-jena.de/software/plums). 21 PLUMS is an interpretation software that analyzes tandem mass spectra of synthetic polymers. The software assists to identify fragmentation series of homopolymers by determining sum formula for the repeating unit and start‐ as well as end‐groups of the fragments.…”

Section: Resultsmentioning

confidence: 99%

“…MS and MS/MS data were processed using the software Flex Analysis and an isotope pattern calculator from Bruker Daltonics and PLUMS, the previously developed tandem mass data interpretation software (http://bio.informatik.uni-jena.de/software/plums). 21…”

Section: Methodsmentioning

confidence: 99%

ESI, APCI, and MALDI tandem mass spectrometry of poly(methyl acrylate)s: A comparison study for the structural characterization of polymers synthesized via CRP techniques and the software application to analyze MS/MS data

Altuntaş

Krieg

Baumgaertel

et al. 2013

J. Polym. Sci. A Polym. Chem.

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Research in polymer science and engineering is moving from classical methodologies to advanced analytical strategies in which mass spectrometry (MS)-based techniques play a crucial role. The molecular complexity of polymers requires new characterization tools and approaches to elucidate the detailed structural information. In this contribution, a comparison study of poly(methyl acrylate)s (PMA) using different tandem mass spectrometry techniques (ESI, APCI, and MALDI MS/MS) is reported to provide insights into the macromolecular structure with the aid of a special MS/MS data interpretation software. Collision-induced dissociation (CID) was utilized to examine the fragmentation pathways of PMAs synthesized via various controlled radical polymerization techniques. All three mass spectrometry techniques are used to analyze structural details of PMAs and the labile end-groups are determined based on the fragmentation behavior in CID. Fragmentation products were identified which are characteristics for the cleavage between the polymer chain and the endgroup. The application of a tailor-made software is shown to analyze complex MS/MS data, and it is proven that this kind of software will be helpful for polymer scientists to identify fragmentation products obtained by tandem mass spectrometry similar to the fields of proteomics, metabolomics, genomics, and glycomics.

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“…Yet, the adaptation of these relatively mature tools for polymer chemistry is still limited, as highlighted by the large number of communications using custom, in‐house written programs . A limited number of open‐source “polymer‐friendly” software packages have been reported to date, including Polymerator, PLUMS, MassChrom2D and COCONUT . The first two programs are angled toward tandem MS data interpretation, while the latter two are restricted to polymer chemical composition analysis and visualization.…”

Section: Introductionmentioning

confidence: 99%

MSPolyCalc: A web‐based App for polymer mass spectrometry data interpretation. The case study of a pharmaceutical excipient

Desport

Frache

Patiny³

2020

Rapid Comm Mass Spectrometry

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Rationale In contrast to biological polymers, synthetic macromolecules consist of distributions of sizes, chemical compositions, functionalities and eventually architectures. The mass spectrum of a synthetic polymer may exhibit a tremendous number of signals. The availability of suitable IT tools to support interpretation is key. Methods A web‐based tool is presented: MSPolyCalc. It offers a set of functionalities, including the calculation of polymer distributions, molecular formulae and a match evaluation for peak assignment based on both mass and spectral accuracy (similarity score). The software was successfully tested with mass spectra exhibiting resolutions ranging from 10,000 to 240,000. Results The molecular characterization of a synthetic poly(ethylene glycol)‐based excipient was achieved. MSPolyCalc allowed the discrimination of six polymer compositions of variable relative abundance. Secondary ionization adducts with very low intensity consisting of matrix‐analyte clusters were also successfully identified. Conclusions MSPolyCalc offers assisted data interpretation to target the needs of polymer chemists. It facilitates structure characterization, ionization adduct identification, and end‐group determination together with visual result reporting.

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Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra

Cited by 13 publications

References 24 publications

Computational mass spectrometry for small molecules

Computational mass spectrometry for small molecules

ESI, APCI, and MALDI tandem mass spectrometry of poly(methyl acrylate)s: A comparison study for the structural characterization of polymers synthesized via CRP techniques and the software application to analyze MS/MS data

MSPolyCalc: A web‐based App for polymer mass spectrometry data interpretation. The case study of a pharmaceutical excipient

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