Electroporation and Mass Spectrometry: A New Paradigm for In Situ Analysis of Intact Proteins Direct from Living Yeast Colonies

A low-voltage alternant direct current electroporation chip for ultrafast releasing the genome DNA of Helicobacter pylori bacterium

Nucleic acid detection, as an important molecular diagnostic method, is widely used in bacterial identification, disease diagnosis. For detecting the nucleic acid of bacteria, the prerequisite is to release nucleic acids inside the bacteria. The common means to release nucleic acids is the chemical method, which involves complex processes, is time-consuming, and remains chemical inhibitors. Compared with chemical methods, electroporation as a physical method has the advantages of easy operation, short-time consumption, and chemical reagents free. However, the current works using electroporation often necessitates high-frequency or high-voltage conditions, entailing bulky power devices. Herein, we propose a low-voltage alternant direct current (LADC) electroporation chip and the corresponding miniature device for ultrafast releasing the genome DNA from Helicobacter pylori (H. pylori) for detection. We connected a micrometer-interdigital electrode in the chip with a 20 V portable battery to make the miniature device. Using this low-voltage device, our chip released genome DNA of H. pylori within only 5 ms, achieving a cell lysis rate of 99.5%. We further combined this chip with a colorimetric loop-mediated isothermal amplification assay to visually detect H. pylori within ~ 25 min at 10 CFU/μL. We detected 11 clinical samples using the chip, and the detection results were consistent with those of the clinical standard. The results indicate that the LADC electroporation chip is useful for ultrafast release of genome DNA from bacteria and is expected to promote the development of nucleic acid detection in POCT and other scenarios.

Surface-sampling mass spectrometry to study proteins and protein complexes

This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.

Native ambient mass spectrometry of intact protein assemblies directly from Escherichia coli colonies

Here, we demonstrate that by combining electroporation with native ambient mass spectrometry, it is possible to detect intact non-covalent protein complexes directly from bacterial colonies growing on agar. Homodimers HdeA and HdeB were identified, together with the 50 kDa Mn-bound superoxide dismutase homodimer, in addition to some previously undetected monomeric proteins.

Applications of ambient ionization mass spectrometry in 2020: An annual review

Recent developments in mass spectrometry (MS) analyses have seen a concerted effort to reduce the complexity of analytical workflows through the simplification (or removal) of sample preparation and the shortening of run-to-run analysis times. Ambient ionization mass spectrometry (AIMS) is an exemplar MS-based technology that has swiftly developed into a popular and powerful tool in analytical science. This increase in interest and demonstrable applications is down to its capacity to enable the rapid analysis of a diverse range of samples, typically in their native state or following a minimalistic sample preparation approach. The field of AIMS is constantly improving and expanding, with developments of powerful and novel techniques, improvements to existing instrumentation, and exciting new applications added with each year that passes. This annual review provides an overview of applications of AIMS techniques over the past year (2020), with a particular focus on the application of AIMS in a number of key fields of research including biomedical sciences, forensics and security, food sciences, the environment, and chemical synthesis. Novel ambient ionization techniques are introduced, including picolitre pressure-probe electrospray ionization and fiber spray ionization, in addition to modifications and improvements to existing techniques such as hand-held devices for ease of use, and USB-powered ion sources for on-site analysis. In all, the information provided in this review supports the view that AIMS has become a leading approach in MS-based analyses and that improvements to existing methods, alongside the development of novel approaches, will continue across the foreseeable future.

Mass Spectrometry Analysis of Intact Proteins from Crude Samples

Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.

Saccharomyces cerevisiae and S. pastorianus species and strain differentiation by direct analysis in real time time-of-flight mass spectrometry

RATIONALE

Seventeen different dried yeast strains, including twelve strains of Saccharomyces cerevisiae and five strains of S. pastorianus, were analyzed using direct analysis in real time (DART) time-of-flight mass spectrometry. The resulting mass spectra were used for rapid species and strain differentiation based upon small-molecule metabolomic profiles.

METHODS

Yeast strains purchased from local shops were suspended in a 1:1 water-methanol solution. Solutions were sampled by dipping the sealed end of a melting point capillary into each vial. Six replicates were measured in positive-ion and negative-ion mode for each strain using an automated linear rail with the DART source operated with helium gas and a gas heater temperature of 350°C. Averaged and centroided mass spectra were exported for analysis with chemometric software.

RESULTS

Negative-ion DART mass spectra exhibited less chemical background and more distinctive components than positive-ion DART mass spectra. An on-line search of the Yeast Metabolome Database provided candidate metabolites for selection as features for chemometric analysis. Negative-ion DART mass spectra could distinguish both species and all strains. The DART analysis was also able to identify potential metabolomic differences between top-fermenting and bottom-fermenting yeast, between beer and baking yeast, and between red wine and champagne yeast.

CONCLUSIONS

All strains could be distinguished by their negative-ion DART mass spectra with 97.7% validation accuracy. Clear differences were observed between dry and liquid forms and Saccharomyces strains with different applications to baking or beverage fermentation. Possible differences in metabolite profiles were suggested, but not confirmed, by accurate mass data.