Introducing π-HelixNovo for practical large-scale de novo peptide sequencing.

De novo peptide sequencing is a promising approach for novel peptide discovery, highlighting the performance improvements for the state-of-the-art models. The quality of mass spectra often varies due to unexpected missing of certain ions, presenting a significant challenge in de novo peptide sequencing. Here, we use a novel concept of complementary spectra to enhance ion information of the experimental spectrum and demonstrate it through conceptual and practical analyses. Afterward, we design suitable encoders to encode the experimental spectrum and the corresponding complementary spectrum and propose a de novo sequencing model $\pi$-HelixNovo based on the Transformer architecture. We first demonstrated that $\pi$-HelixNovo outperforms other state-of-the-art models using a series of comparative experiments. Then, we utilized $\pi$-HelixNovo to de novo gut metaproteome peptides for the first time. The results show $\pi$-HelixNovo increases the identification coverage and accuracy of gut metaproteome and enhances the taxonomic resolution of gut metaproteome. We finally trained a powerful $\pi$-HelixNovo utilizing a larger training dataset, and as expected, $\pi$-HelixNovo achieves unprecedented performance, even for peptide-spectrum matches with never-before-seen peptide sequences. We also use the powerful $\pi$-HelixNovo to identify antibody peptides and multi-enzyme cleavage peptides, and $\pi$-HelixNovo is highly robust in these applications. Our results demonstrate the effectivity of the complementary spectrum and take a significant step forward in de novo peptide sequencing.

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis.

Multiplexed quantitative proteomics using tandem mass tag (TMT) is increasingly used in -omic study of complex samples. While TMT-based proteomics has the advantages of the higher quantitative accuracy, fewer missing values, and reduced instrument analysis time, it is limited by the additional reagent cost. In addition, current TMT labeling workflows involve repeated small volume pipetting of reagents in volatile solvents, which may increase the sample-to-sample variations and is not readily suitable for high throughput applications. In this study, we demonstrated that the TMT labeling procedures could be streamlined by using pre-aliquoted dry TMT reagents in a 96 well plate or 12-tube strip. As little as 50 µg dry TMT per channel was used to label 6-12 µg peptides, yielding high TMT labeling efficiency (∼99%) in both microbiome and mammalian cell line samples. We applied this workflow to analyze 97 samples in a study to evaluate whether ice recrystallization inhibitors improve the cultivability and activity of frozen microbiota. The results demonstrated tight sample clustering corresponding to groups and consistent microbiome responses to prebiotic treatments. This study supports the use of TMT reagents that are pre-aliquoted, dried, and stored for robust quantitative proteomics and metaproteomics in high throughput applications.

MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database.

The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools. Here we develop MetaLab-MAG, a specially designed tool for the characterization of microbiomes from metagenome-assembled genomes databases. MetaLab-MAG was evaluated by analyzing various human gut microbiota data sets and performed comparably or better than searching the gene catalog protein database directly. MetaLab-MAG can quantify the genome-level microbiota compositions and supports both label-free and isobaric labeling-based quantification strategies. MetaLab-MAG removes the obstacles of metaproteomic data analysis and provides the researchers with in-depth and comprehensive information from the microbiomes.

Assessing the Dark Field of Metaproteome.

The human gut microbiome is a complex system composed of hundreds of species, and metaproteomics can be used to explore their expressed functions. However, many lower abundance species are not detected by current metaproteomic techniques and represent the dark field of metaproteomics. We do not know the minimal abundance of a bacterium in a microbiome(depth) that can be detected by shotgun metaproteomics. In this study, we spiked 15N-labeled E. coli peptides at different percentages into peptides mixture derived from the human gut microbiome to evaluate the depth that can be achieved by shotgun metaproteomics. We observed that the number of identified peptides and peptide intensity from 15N-labeled E. coli were linearly correlated with the spike-in levels even when 15N-labeled E. coli was down to 0.5% of the biomass. Below that level, it was not detected. Interestingly, the match-between-run strategy significantly increased the number of quantified peptides even when 15N-labeled E. coli peptides were at low abundance. This is indicative that in metaproteomics of complex gut microbiomes many peptides from low abundant species are likely observable in MS1 but are not selected for MS2 by standard shotgun strategies.

Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface.

Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.

pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies.

MOTIVATION: Enzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent-proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting difficulties with protein and functional assignment. RESULTS: To combat this challenge, we developed pepFunk, a peptide-centric metaproteomic workflow focused on the analysis of human gut microbiome samples. Our workflow includes a curated peptide database annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG) terms and a gene set variation analysis-inspired pathway enrichment adapted for peptide-level data. Analysis using our peptide-centric workflow is fast and highly correlated to a protein-centric analysis, and can identify more enriched KEGG pathways than analysis using protein-level data. Our workflow is open source and available as a web application or source code to be run locally. AVAILABILITY AND IMPLEMENTATION: pepFunk is available online as a web application at https://shiny.imetalab.ca/pepFunk/ with open-source code available from https://github.com/northomics/pepFunk. CONTACT: dfigeys@uottawa.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fabrication of Vertical-Standing Co-MOF Nanoarrays with 2D Parallelogram-like Morphology for Aqueous Asymmetric Electrochemical Capacitors.

Metal organic frameworks (MOFs) have been considered as one of the most promising electrode materials for electrochemical capacitors due to their large specific surface area and abundant pore structure. Herein, we report a Co-MOF electrode with a vertical-standing 2D parallelogram-like nanoarray structure on a Ni foam substrate via a one-step solvothermal method. The as-prepared Co-MOF on a Ni foam electrode delivered a high area-specific capacitance of 582.0 mC cm-2 at a current density of 2 mA cm-2 and a good performance rate of 350.0 mC cm-2 at 50 mA cm-2. Moreover, an asymmetric electrochemical capacitor (AEC) device (Co-MOF on Ni foam//AC) was assembled by using the as-prepared Co-MOF on a Ni foam as the cathode and a active carbon-coated Ni foam as the anode to achieve a maximum energy density of 0.082 mW cm-2 at a power density of 0.8 mW cm-2, which still maintained 0.065 mW cm-2 at a high power density of 11.94 mW cm-2. Meanwhile, our assembled device exhibited an excellent cycling stability with a capacitance retention of nearly 100% after 1000 cycles. Therefore, this work provides a simple method to prepare MOF-based material for the application of energy storage and conversion.

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics.

Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics provides invaluable functional information on the state of a microbiome. However, lower-abundance bacteria in complex microbiomes are difficult to observe by metaproteomics. In this study, stepwise differential lysis protocols were developed for human stool microbiomes to separate different microbial species and to increase the depth of metaproteomic measurements. We achieved differential lysis of Gram-positive (G+) and Gram-negative (G-) bacteria, selective enrichment of specific bacteria, and functional enrichment by our stepwise differential lysis protocols. Therefore, differential lysis can serve as a fractionation method to reduce sample complexity and selectively extract proteins from specific taxa for deep metaproteomic studies.

Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation.

Glycosylation is one of the most important post-translational modifications in biological systems. Current glycoproteome methods mainly focus on qualitative identification of glycosylation sites or intact glycopeptides. However, the systematic quantitation of glycoproteins has remained largely unexplored. Here, we developed a chemoenzymatic method to quantitatively investigate N-glycoproteome based on the N-glycan types. Taking advantage of the specificity of different endoglycosidases and isotope dimethyl labeling, six N-glycan types of structures linked on each glycopeptide, including high-mannose/hybrid, biantennary, and triantennary with/without core fucose, were quantified. As a proof of principle, the glycoproteomic N-glycan type quantitative (glyco-TQ) method was first used to determine the N-glycan type composition of the immunoglobulin G1 (IgG1) Fc fragment. Then we applied the method to analyze the glycan type profile of proteins from the breast cancer cell line MCF7, and we quantitatively revealed the N-glycan type microheterogeneity at the glycopeptide and glycoprotein level. The novel quantitative strategy to evaluate the relative intensity of the six states of N-glycan type glycosylation on each site provides a new avenue to investigate the function of glycoproteins in broad areas, such as cancer biomarker research, pharmaceuticals characterization, and antiglycan vaccine development.

iMetaLab 1.0: a web platform for metaproteomics data analysis.

Summary: The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry data remains a daunting task in metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for metaproteomics data analysis. Availability and implementation: iMetaLab is freely available through at http://imetalab.ca. Supplementary information: Supplementary data are available at Bioinformatics online.

Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach.

In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.

The influence of bioregenerative life-support system dietary structure and lifestyle on the gut microbiota: a 105-day ground-based space simulation in Lunar Palace 1.

Understanding the dynamics of human gut microbiota in space is crucial in maintaining astronaut health. Long-duration and deep-space manned exploration will require the in situ regeneration of resources, which would be achieved by an artificial ecosystem, such as a bioregenerative life-support system (BLSS). Potential response of human gut microbiota to particular lifestyle and dietary structure experienced in a BLSS remains unclear. Here, we report how a BLSS impacts the gut microbiota during a 105-day study that took place in the Chinese Lunar Palace 1 (LP1). The three crewmembers were provided with high-plant and high-fibre diet, and they followed a fixed schedule including extensive labour in the plant cabin. The gut microbiota composition of the three crewmembers showed convergence and similar dynamic change. Increased diversity and abundance of Lachnospira, Faecalibacterium and Blautia indicated that the LP1 dietary structure and the lifestyle may be beneficial for the maintenance of healthy gut microbiome. A stronger impact was found from the gut microbiome to the environment compared with the opposite direction, suggesting the necessity of environmental pathogen control in BLSS.

Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.

The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics.

Aim: Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol. Methods: To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on ex vivo individual human gut microbiomes biobanked with five different workflows. Results: We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, in vitro culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose. Conclusions: Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.

Self-Assembled MXene@Fluorographene Hybrid for High Dielectric Constant and Low Loss Ferroelectric Polymer Composite Films.

Modern electrical applications urgently need flexible polymer films with a high dielectric constant (εr) and low loss. Recently, the MXene-filled percolative composite has emerged as a potential material choice because of the promised high εr. Nevertheless, the typically accompanied high dielectric loss hinders its applications. Herein, a facile and effective surface modification strategy of cladding Ti3C2Tx MXene (T = F or O; FMX) with fluorographene (FG) via self-assembly is proposed. The obtained FMX@FG hybrid yields high εr (up to 108 @1 kHz) and low loss (loss tangent tan δ = 1.16 @ 1 kHz) in a ferroelectric polymer composite at a low loading level (the equivalent of 1.5 wt % FMX), which is superior to its counterparts in our work (e.g., FMX: εr = 104, tan δ = 10.71) and other studies. It is found that the FG layer outside FMX plays a critical role in both the high dielectric constant and low loss from experimental characterizations and finite element simulations. For one thing, FG with a high F/C ratio would induce a favorable structure of high ß-phase crystallinity, extensive microcapacitor networks, and abundant interfacial dipoles in polymer composites that account for the high εr. For another, FG, as a highly insulating layer, can inhibit the formation of conductive networks and inter-FMX electron tunneling, which is responsible for conduction loss. The results demonstrate the potential of a self-assembled FMX@FG hybrid for high εr and low loss polymer composite films and offer a new strategy for designing advanced polymer composite dielectrics.

Molecular characterization of hybrid virulence plasmids in ST11-KL64 KPC-2-producing multidrug-resistant hypervirulent Klebsiella pneumoniae from China.

Introduction: Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-HvKP) strains combining virulence and multidrug resistance (MDR) features pose a great public health concern. The aim of this study is to explore the evolutionary characteristics of virulence in CR-HvKP by investigating the genetic features of resistance and virulence hybrid plasmids. Methods: The resistance and virulence phenotypes were determined by using antimicrobial susceptibility testing and the mouse bacteremia infection model, respectively. Plasmid profiles were investigated by S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting, conjugation assay, and whole genome sequencing (WGS). Bioinformatics tools were used to uncover the genetic features of the resistance and virulence hybrid plasmids. Results: Two ST11-KL64 CRKP clinical isolates (KP18-3-8 and KP18-2079), which exhibited enhanced virulence compared with the classic CRKP, were detected positive for blaKPC-2 and rmpA2. The virulence level of the hypermucoviscous strain KP18-3-8 was higher than that of KP18-2079. S1-PFGE, Southern hybridization and WGS analysis identified two novel hybrid virulence plasmids in KP18-3-8 (pKP1838-KPC-vir, 228,158 bp) and KP18-2079 (pKP1838-KPC-vir, 182,326 bp), respectively. The IncHI1B/repB-type plasmid pKP1838-KPC-vir co-harboring blaKPC-2 and virulence genes (rmpA2, iucABCD and iutA) but lacking type IV secretion system could transfer into non-hypervirulent ST11 K. pneumoniae with the assistance of a helper plasmid in conjugation. The IncFII/IncR-type virulence plasmid pKP18-2079-vir may have been generated as a result of recombination between a typical pLVPK-like virulence plasmid and an MDR plasmid. Conclusion: Our studies further highlight co-evolution of the virulence and resistance plasmids in ST11-CRKP isolates. Close surveillance of such hybrid virulence plasmids in clinical K. pneumoniae should be performed.

All-natural 2D nanofluidics as highly-efficient osmotic energy generators.

Two-dimensional nanofluidics based on naturally abundant clay are good candidates for harvesting osmotic energy between the sea and river from the perspective of commercialization and environmental sustainability. However, clay-based nanofluidics outputting long-term considerable osmotic power remains extremely challenging to achieve due to the lack of surface charge and mechanical strength. Here, a two-dimensional all-natural nanofluidic (2D-NNF) is developed as a robust and highly efficient osmotic energy generator based on an interlocking configuration of stacked montmorillonite nanosheets (from natural clay) and their intercalated cellulose nanofibers (from natural wood). The generated nano-confined interlamellar channels with abundant surface and space negative charges facilitate selective and fast hopping transport of cations in the 2D-NNF. This contributes to an osmotic power output of ~8.61 W m-2 by mixing artificial seawater and river water, higher than other reported state-of-the-art 2D nanofluidics. According to detailed life cycle assessments (LCA), the 2D-NNF demonstrates great advantages in resource consumption (1/14), greenhouse gas emissions (1/9), and production costs (1/13) compared with the mainstream 2D nanofluidics, promising good sustainability for large-scale and highly-efficient osmotic power generation.

Cuboid-like phosphorus-doped metal-organic framework-derived CoSe2 on carbon cloth as an advanced bifunctional oxygen electrocatalyst for rechargeable zinc-air batteries.

Zinc-air batteries (ZABs) are regarded as attractive devices for electrochemical energy storage and conversion due to their outstanding electrochemical performance, low price, and high safety. However, it remains a challenge to design a stable and efficient bifunctional oxygen catalyst that can accelerate the reaction kinetics and improve the performance of ZABs. Herein, a phosphorus-doped transition metal selenide/carbon composite catalyst derived from metal-organic frameworks (P-CoSe2/C@CC) is constructed by a self-supporting carbon cloth structure through a simple solvothermal process with subsequent selenization and phosphatization. The P-CoSe2/C@CC exhibits a low overpotential of 303.1 mV at 10 mA cm-2 toward the oxygen evolution reaction and an obvious reduction peak for the oxygen reduction reaction. The abovementioned electrochemical performances for the P-CoSe2/C@CC are attributed to the specific architecture, the super-hydrophilic surface, and the P-doping effect. Remarkably, the homemade zinc-air battery based on our P-CoSe2/C@CC catalyst shows an expected peak power density of 124.4 mW cm-2 along with excellent cycling stability, confirming its great potential application in ZABs for advanced bifunctional electrocatalysis.