scholarly journals Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254429
Author(s):  
Yuanyue Li ◽  
Michael Kuhn ◽  
Joanna Zukowska-Kasprzyk ◽  
Marco L. Hennrich ◽  
Panagiotis L. Kastritis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Metabolite Identification ◽  
Thermophilic Fungus ◽  
Chaetomium Thermophilum ◽  
Isopentenyl Adenine ◽  
Cell Fractions ◽  
Biological State ◽  
Proof Of Principle

Protein–metabolite interactions play an important role in the cell’s metabolism and many methods have been developed to screen them in vitro. However, few methods can be applied at a large scale and not alter biological state. Here we describe a proteometabolomic approach, using chromatography to generate cell fractions which are then analyzed with mass spectrometry for both protein and metabolite identification. Integrating the proteomic and metabolomic analyses makes it possible to identify protein-bound metabolites. Applying the concept to the thermophilic fungus Chaetomium thermophilum, we predict 461 likely protein-metabolite interactions, most of them novel. As a proof of principle, we experimentally validate a predicted interaction between the ribosome and isopentenyl adenine.

scholarly journals Interoperable and scalable data analysis with microservices: Applications in Metabolomics

2017 ◽  
Author(s):  
Payam Emami Khoonsari ◽  
Pablo Moreno ◽  
Sven Bergmann ◽  
Joachim Burman ◽  
Marco Capuccini ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Large Scale ◽  
Metabolite Identification ◽  
Access Point ◽  
Scientific Discipline ◽  
Resonance Spectroscopy ◽  
Magnetic Resonance Spectroscopy Study ◽  
Analysis Workflow ◽  
Computational Resources

Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed in parallel using the Kubernetes container orchestrator. The access point is a virtual research environment which can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and established workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry studies, one nuclear magnetic resonance spectroscopy study and one fluxomics study, showing that the method scales dynamically with increasing availability of computational resources. We achieved a complete integration of the major software suites resulting in the first turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, multivariate statistics, and metabolite identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.

scholarly journals Cell-based meat: the need to assess holistically

2020 ◽  
Vol 98 (8) ◽  
Author(s):  
Cameron Faustman ◽  
Deb Hamernik ◽  
Michael Looper ◽  
Steven A Zinn
Keyword(s):  
Knowledge Base ◽  
Muscle Tissue ◽  
Manufacturing Process ◽  
Cell Biology ◽  
Large Scale ◽  
New Product ◽  
Subsequent Research ◽  
Potential Alternative ◽  
Proof Of Principle

Abstract Proof-of-principle for large-scale engineering of edible muscle tissue, in vitro, was established with the product’s introduction in 2013. Subsequent research and commentary on the potential for cell-based meat to be a viable food option and potential alternative to conventional meat have been significant. While some of this has focused on the biology and engineering required to optimize the manufacturing process, a majority of debate has focused on cultural, environmental, and regulatory considerations. Animal scientists and others with expertise in muscle and cell biology, physiology, and meat science have contributed to the knowledge base that has made cell-based meat possible and will continue to have a role in the future of the new product. Importantly, the successful introduction of cell-based meat that looks and tastes like conventional meat at a comparable price has the potential to displace and/or complement conventional meat in the marketplace.

Screening Tagged Proteins Using Tandem Affinity-Buffer Exchange Chromatography Online with Native Mass Spectrometry

2021 ◽  
Author(s):  
Florian Busch ◽  
Zachary VanAernum ◽  
Stella M. Lai ◽  
Venkat Gopalan ◽  
Vicki Wysocki
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Tertiary Structure ◽  
Direct Analysis ◽  
Native Mass Spectrometry ◽  
Exchange Chromatography ◽  
Size Exclusion ◽  
Functional Protein ◽  
Translation Rate

Protein overexpression and purification are critical for in vitro structure-function characterization studies. However, some proteins are difficult to express robustly in heterologous systems due to host-related (e.g., codon usage, translation rate) and/or protein specific (e.g., toxicity, aggregation) challenges. Therefore, it is often necessary to screen<br>multiple overexpression and purification conditions to maximize the yield of functional protein, particularly for resource-heavy downstream applications (e.g., biocatalysts, tertiary structure determination, biotherapeutics). Here, we describe an automatable liquid chromatography–mass spectrometry-based method for rapid, direct analysis of target proteins in cell lysates. This online approach is facilitated by coupling immobilized metal affinity chromatography (IMAC), which leverages engineered poly-histidine tags in proteins of interest, with size exclusion-based buffer exchange (OBE) and native mass spectrometry (nMS). The use of IMAC-OBE-nMS to optimize conditions for large-scale protein production should expedite structural biology and biotherapeutic initiatives.<br>

Rapid Identification of Commercial Frankincense Products by MALDI-TOF Mass Spectrometry

2021 ◽  
Vol 24 ◽  
Author(s):  
Shang-Chih Lai ◽  
Ren-In You ◽  
Tz-Ting Chen ◽  
Yu Chang ◽  
Chao-Zong Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
Reference Sample ◽  
Maldi Tof Ms ◽  
Boswellic Acids ◽  
Maldi Tof ◽  
Tof Ms

Background: Frankincense is a resin secreted by the Boswellia tree. It is used in perfumery, aromatherapy, skincare, and traditional Chinese medicine. However, all Boswellia species are under threat owing to habitat loss and overexploitation. As a result, the market is getting flooded with counterfeit frankincense products. Objective: This study aims to establish a high-throughput method to screen and identify the authenticity of commercial frankincense products. We report, for the first time, a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based method for rapid and high-throughput screening of frankincense samples. Methods: MALDI-TOF MS, HPLC, thin-layer chromatography (TLC), and in vitro anti-inflammatory activity assay were used to examine the frankincense samples. Results: Well-resolved peaks of frankincense triterpenoids in the spectra were observed in the crude extract of commercial samples, including α-boswellic acids (αBAs), β-boswellic acids (βBAs), 11-keto-β-boswellic acids (KBAs), acetyl-11-keto-β-boswellic acids (AKBAs), and their esters. These compounds can be used as indicators for determining the authenticity of frankincense. Conclusion: Unlike LC–MS, which is a time-consuming and expensive method, and TLC, which requires a reference sample, our inexpensive, rapid high-throughput identification method based on MALDI-TOF MS is ideal for large-scale screening of frankincense samples sold in the market.

scholarly journals In vitro metabolite identification of Tamsulosin using LC-Q-TOF mass spectrometry

2018 ◽  
Vol 5 (1) ◽  
pp. 165-171
Author(s):  
Sai Laxmi Kesana ◽  
Dodle Jaya Prakash, ◽  
Vamaraju Harinadha Babu ◽  
P.C . Sastry
Keyword(s):  
Mass Spectrometry ◽  
Metabolite Identification
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