Application of MALDI Mass Spectrometry in Natural Products Analysis

Silva, Ricardo; Lopes, Norberto Peporine; Silva, Denise Brentan

doi:10.1055/s-0042-104800

Cited by 37 publications

(31 citation statements)

References 234 publications

(279 reference statements)

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“…IDBac is open source and the code is available for anyone to customize their data analysis and visualization needs. We recommend that users consult an extensive body of literature (Sauer et al 7 , Silva et al 5 ) to help support and design their experimental goals. We host a forum for discussion at: https://groups.google.com/forum/#!forum/idbac and a means to report issues with the software at: https://github.com/chasemc/ IDBacApp/issues.…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, information on specialized metabolite production, a major driver of microbial function in the environment, has remained unincorporated in these studies. Silva et al 5 recently provided a comprehensive history detailing the underuse of MALDI-TOF MS to analyze specialized metabolites and the shortage of software to relieve current bioinformatics bottlenecks. In order to address these shortcomings, we created IDBac, a bioinformatics pipeline that integrates both linear and reflectron modes of MALDI-TOF MS 6 .…”

Section: Introductionmentioning

confidence: 99%

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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Clark

Costa

Conley

et al. 2019

JoVE

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In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Clark

Costa

Conley

et al. 2019

JoVE

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“…Brazil has a rich history of phytochemical investigation but for many years a major component of these studies was directed towards identification of plant metabolites and structure determination, with examples being the paper by Regasini et al, 71 and one published the previous year on chemical constituents of flowers from Pterogyne nitens also by Regasini et al 72 To these can be added the excellent paper on the use of modern mass spectral techniques in determining chemical structures from Silva et al 73 More and more papers have been published where biological activities of isolated compounds were reported including the use of bioactivity driven isolation techniques. A recent example would be the report on the discovery of cytotoxic guanidine alkaloids from the same plant species as mentioned above.…”

Section: General Commentsmentioning

confidence: 99%

The Influence of Brazilian Biodiversity on Searching for Human Use Pharmaceuticals

Newman¹

2016

J. Braz. Chem. Soc.

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This relatively short review will cover the history of some potential drug entities whose beginnings were from Brazilian flora and fauna that led to scientific findings many years later that could not even have been thought of at the time of their initial discovery. The first two are the discoveries of the effects of peptidic toxins from the highly poisonous snake Bothrops jararaca upon the control of bradykinins that led to the angiotensin converting enzyme inhibitors, and the identification of pederin from the blister beetle Paederus species that 50 plus years later led to brand new discoveries as the source of many marine sponge metabolites. All occurred well before the Convention on Biological Diversity (CBD), in 1992. Then come discussions on lapachol and its congeners and then the potential for the investigation of microbes that are associated with insects, plants and marine invertebrates and their control of the syntheses of novel metabolites with pharmaceutical potential. The review finishes with comments on the biodiversity programs that São Paulo State has put in place and how they are materially aiding in investigations of Brazilian flora and fauna but under conditions that are CBD-compliant.

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“…In addition to linear mode protein analysis, we employ reflectron mode to analyze specialized metabolites, as the combination of both information-rich spectral regions has yet to be applied to existing MALDI-TOF MS analysis pipelines. Silva et al recently provided a comprehensive history detailing the relatively limited use of MALDI MS to analyze specialized metabolites (20).…”

Section: Introductionmentioning

confidence: 99%

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

Clark

Costa

Sanchez

et al. 2017

Preprint

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For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra of single bacterial colonies from agar plates. We demonstrated the power of our approach by discriminating between two Bacillus subtilis colonies in under 30 minutes, which differ by a single genomic mutation, solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin. Next, we employed our IDBac technique to detect subtle intra-species differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwater Micromonospora isolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we employed our method to simultaneously extract protein and specialized metabolite MS profiles from unidentified species of Lake Michigan sponge-associated bacteria cultivated on an agar plate. In just 3 hours, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 samples) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on inter- and intra-species differences in specialized metabolite production. To our knowledge, IDBac is the first attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow the distinction of closely related bacterial colonies.SignificanceMass spectrometry is a powerful technique that has been used to identify bacteria via protein content, and to assess bacterial function in an environment via analysis of specialized metabolites. However, until now these analyses have operated independently, and this has resulted in the inability to rapidly connect bacterial phylogenetic identity with patterns of specialized metabolism. To bridge this gap, we designed a MALDI-TOF mass spectrometry data acquisition and bioinformatics pipeline (IDBac) to discriminate both intact protein and specialized metabolite spectra directly from bacterial cells grown on agar. To our knowledge, this is the first technique that organizes bacteria into highly similar phylogenetic groups and allows for comparison of metabolic differences of hundreds of isolates in just a few hours.

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Application of MALDI Mass Spectrometry in Natural Products Analysis

Cited by 37 publications

References 234 publications

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

The Influence of Brazilian Biodiversity on Searching for Human Use Pharmaceuticals

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

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