Biology subjects

Zamboni, N.

Publications and source records attributed to Zamboni, N..

At least 19 recordsLinked to original sources

bioRxiv2026

ChEBI-N - Enrichment Analysis with the ChEBI Ontology

Introduction: Biological and chemical ontologies are structured representations that can be used to map entities such as metabolites onto broader chemical and biological categories. Enrichment analysis applied to such ontologies identifies classes whose representation within a set deviates from an expected background distribution, helping to interpret complex metabolomics measurements. Objectives: This study aimed to develop a tool for ChEBI (Chemical Entities of Biological Interest) ontology-based enrichment analysis, named ChEBI-N (ChEBI eNrichment). It is a successor of the previous tool BiNChE, with new features that broaden its applicability. Methods: We reimplemented BiNChE and extended it to accept SMILES or InChI strings as well as ChEBI IDs. These broaden applicability to datasets with entities that are not yet present in ChEBI. We also constructed organism-specific background populations. Results: We demonstrate the tool on three published metabolomics datasets covering wine, cheese, and human plasma samples. ChEBI-N correctly highlighted relevant enriched classes in all three datasets, such as flavonoids in the wine dataset and fatty acid classes in the cheese dataset. Comparing organism-specific and full-ChEBI backgrounds shows that restricted backgrounds reduce the inflated significance of generic classes, although the most enriched classes remain largely consistent. Conclusion: ChEBI-N is an extended successor to BiNChE for ontology-based enrichment analysis of metabolomics data, offering a hypothesis-generating complement to existing metabolomics analysis pipelines. Availability: ChEBI-N is freely available at chebin.hastingslab.org or as a Python package (pypi.org/project/chebin), with source code at github.com/ontology-tools/chebin, archived at Zenodo (doi:10.5281/zenodo.23264219) and Software Heritage (swh:1:rev:133a41792704eb7f1db746f36a5ae97e9247b2b7).

bioinformatics↗

bioRxiv2026

Multi-omics integration identifies a reproducible inflammatory host-response axis in pediatric sepsis

Sepsis is a major cause of morbidity and mortality in children, yet biological heterogeneity in host responses has limited progress toward targeted therapies and patient stratification. Multiomics integration can combine complementary molecular layers to identify coordinated disease programs not captured by individual assays. Here, we integrated genomic, bulk transcriptomic, proteomic and metabolomic data from blood samples of 22 children with culture-confirmed bacterial sepsis enrolled in the Swiss Pediatric Sepsis Study. Multi-Omics Factor Analysis identified a dominant host-response axis reflecting systemic inflammation. This axis was driven primarily by transcriptomic variation and supported by coordinated proteomic and metabolomic signals, including circulating inflammatory mediators and altered amino-acid metabolism. It was associated with C-reactive protein and a severity score proxy. Projection into an independent pediatric sepsis cohort (n = 22) reproduced the inflammatory and severity-related interpretation of this axis. Single-omic projections showed that the integrated signal could be approximated from individual layers, particularly transcriptomics. In three external pediatric whole-blood transcriptomic datasets, the RNA-derived projection separated septic shock from healthy controls and increased across clinical inflammatory syndromes. These findings define a reproducible inflammatory host-response axis in pediatric sepsis and support multi-omics-guided selection of molecular readouts suitable for clinical translation.

immunology↗

bioRxiv2025

Systematic structural and functional analysis of metal-binding sites in native proteomes

Metal-binding proteins (MBPs) are widespread and critical for many biological processes. Proteomics-based approaches have identified MBPs in various systems but typically cannot determine the location of metal-binding sites or shed light on the functional roles of metals. Thus, a systems-wide map of metal binding sites and an understanding of the consequences of metal binding for protein function are still lacking. Here, we used limited proteolysis-coupled mass spectrometry (LiP-MS) combined with chelator treatment to globally map metal-protein interactions and binding sites in native protein lysates. We applied the pipeline, named Metal-LiP, to Escherichia coli, identified 981 peptides on 297 proteins that exhibited dose responsiveness to chelator treatment, and quantified the relative metal-binding affinity. These proteins are strongly enriched for known or predicted MBPs, based on our novel compiled ground truth dataset of previously annotated (n=1013) and predicted (n=850) MBPs. Further, chelator-responsive peptides mapped at or near annotated metal-binding sites in 3D protein structures, showing that Metal-LiP can identify metal-binding sites, and provided novel experimental evidence for previously predicted sites. Notably, Metal-LiP identified 225 novel candidate MBPs and we validated five of these novel MBPs (GatZ, AhpC, GrxB, MsrC, TrhO) using inductively coupled plasma-mass spectrometry to detect metal binding in purified proteins. Finally, we used orthogonal approaches to probe the broad functional consequences of metal binding. Using a combination of Metal-LiP, thermal proteome profiling, size-exclusion chromatography coupled to mass spectrometry, and structural analyses, we identified cases where metal binding affects protein stability, modulates the assembly states of protein complexes, or is likely to affect enzymatic activity. We thereby propose functional roles for metal binding in 98 of our Metal-LiP hits and in 225 proteins in total. In summary, we describe an approach to identify bona fide MBPs with binding site-level resolution across the proteome. We have combined it with other methods to identify 424 candidate MBPs in the E coli proteome, to map known and novel candidate metal-binding sites for 297 of these proteins, and to suggest functional roles of metal binding.

systems biology↗

bioRxiv2025

Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa

The widespread use of antibiotics promotes both resistance and tolerance. While resistance enables bacterial growth in the presence of drugs, tolerance allows survival during treatment, generating persisters that seed relapse and promote resistance. Despite its clinical relevance, the molecular basis of tolerance remains poorly understood. Using proteomic and metabolomic profiling combined with machine learning, we identified thiol oxidation as a robust predictor of tolerance in the human pathogen Pseudomonas aeruginosa. Single-cell analyses established a direct link between thiol oxidation and drug survival, indicating that redox imbalance drives persistence. Whereas depletion of coenzyme A (CoA), a central thiol-containing metabolite, scaled with tolerance, restoring CoA using engineered catalysts from Staphylococcus aureus abolished tolerance, establishing a causal relation between CoA availability and drug susceptibility. Thiol-based predictors also accurately capture tolerance of clinical P. aeruginosa isolates. These findings establish CoA-centered redox control as a key determinant of tolerance, opening opportunities for diagnostics and therapeutic interventions to prevent infection relapses.

microbiology↗

bioRxiv2025

ACOD1 regulates microglial arginine metabolism and inflammatory responses

Itaconate is produced by inflammatory macrophages and promotes a negative feedback on inflammation. It is synthesized by aconitate decarboxylase 1 (ACOD1) from cis- aconitate, a metabolite of the tricarboxylic acid cycle. Here, we studied the role of ACOD1 in the inflammatory response of microglia, the resident macrophage-like cells of the brain. Similar to macrophages, ACOD1 deficient microglia displayed a stronger inflammatory response to lipopolysaccharide (LPS) compared to their wild type counterparts. The proinflammatory effects of ACOD1 deficiency were associated with reprogramed arginine metabolism entailing enhanced argininosuccinate synthesis at the expense of polyamine synthesis, in a manner that was dependent on ACLY. These findings provide new insights in the immunometabolic role of ACOD1 in inflammatory microglia.

immunology↗

bioRxiv2025

Circulating extracellular vesicles can transport stress signals to the male germline

Extracellular vesicles (EVs) play a key role in cell-cell communication by transporting bioactive molecules from donor to recipient cells across the body. While their involvement in somatic cells communication is well described, somatic-to-germ cells communication remains understudied. We show that small EVs (sEVs) can vehicle signals of early life stress (ELS) from circulation to sperm consequentially for the offspring. In mice, ELS persistently modifies RNA, lipids and metabolites in plasma sEVs. Chronic injection of plasma sEVs from ELS-exposed males alters the sperm transcriptome and is reflected in the transcriptome of embryos. This leads to metabolic dysfunctions in the adult offspring. These findings highlight a role of circulating sEVs in soma-to-germline communication relevant for the intergenerational transmission of ELS effects.

cell biology↗

bioRxiv2025

Multi-omics analysis of endothelial cells reveals the metabolic diversity that underlies endothelial cell functions

Endothelial cells (ECs) line the vascular system and are key players in vascular homeostasis, yet their metabolic diversity across tissues, vascular beds, and growth states remains poorly understood. This study examines metabolic differences between proliferating and quiescent ECs and compares blood and lymphatic endothelium using proteomics and metabolomics. Our findings indicate that metabolism in quiescent ECs is not dormant but reorganized in a cell-specific manner, with decreased heme intermediates in human umbilical vein ECs and increased branched-chain amino acid catabolism across all quiescent ECs. Consistent with the differences identified in the omics data, perturbation studies revealed that inhibiting enzymes involved in heme, glutamate, fatty acid, and nucleotide biosynthesis led to distinct phenotypic responses in blood and lymphatic ECs. These findings highlight the importance of metabolic pathways in sustaining both proliferating and quiescent ECs and reveal how ECs from different vascular beds rely on distinct metabolic processes to maintain their functional states.

systems biology↗

bioRxiv2024

Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease

The involvement of the human intestinal microbiome in the regulation of immune cell homeostasis, as well as in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), are well-established1-4. Bacteria interact with immune cells at the sites of intestinal inflammation, but also in the CRC tumor microenvironment1-6. Indeed, bacterial remnants have recently been detected in human intestinal tissue in patients with IBD, at primary tumor sites and in the metastases of patients with CRC, and in whole blood3,7,8. A defective intestinal epithelial barrier is thought to promote bacterial remnant translocation and disease progression6. However, it is unknown, how bacterial remnants translocate from the intestine to sites of metastasis or into the circulation. We hypothesized that bacterial remnants translocate within peripheral blood immune cells into the circulation. Here, we thus explored the composition of the detectable microbiome in peripheral blood mononuclear cells (PBMCs) of patients with CRC or IBD compared to healthy controls. The PBMC microbiome profiles partially align with the tumor- and metastasis-derived or intestinal tissue-derived microbiome signatures obtained from the same patients with CRC or IBD, respectively. Our metagenomics data, supported by 16S-rRNA-FISH-Flow, imaging flow cytometry and species-specific qPCR, reveal the presence of translocated bacterial genetic sequences in the patients with CRC and IBD, likely due to an intestinal barrier defect. Pathway and serum metabolomics analysis connected to the metabolic potential of the PBMC-derived microbiome sequences support the onset of microbial translocation in such patients. Thus, our data suggest that in patients with intestinal barrier leakage, such as those with CRC or IBD, there is the potential for the translocation of bacterial remnants into the circulation via peripheral immune cells.

cancer biology↗

bioRxiv2023

GLUD1 dictates muscle stem cell differentiation by controlling mitochondrial glutamate levels

Muscle stem cells (MuSCs) enable muscle growth and regeneration after exercise or injury. Upon activation MuSCs metabolically rewire to meet the changing demands of proliferation. Here we describe that primary changes in metabolism itself can dictate MuSC fate decisions to control differentiation and fusion. We found that glutamine anaplerosis into the TCA cycle decreases during MuSC differentiation and coincides with decreased expression of the mitochondrial glutamate deaminase GLUD1. Genetic deletion of Glud1 in proliferating MuSCs resulted in precocious differentiation and imbalanced fusion combined with loss of self-renewal in vitro and in vivo. Mechanistically, deleting Glud1 caused mitochondrial glutamate accumulation in proliferating MuSCs and inhibited the malate-aspartate shuttle (MAS). Restoring MAS activity by supplementation of alanine normalized differentiation. In conclusion, high GLUD1 activity in proliferating MuSCs prevents deleterious mitochondrial glutamate accumulation and inactivation of the MAS. It thereby acts as a compartment specific metabolic brake on MuSC differentiation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/560525v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@e3585dorg.highwire.dtl.DTLVardef@1be4a54org.highwire.dtl.DTLVardef@1f077org.highwire.dtl.DTLVardef@15220f1_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlutamine is the major TCA cycle substrate in MuSCs with decreasing contribution upon differentiation. C_LIO_LILoss of Glud1 impairs MuSC self-renewal capacity and causes imbalanced fusion in vitro and in vivo. C_LIO_LIGlud1 deletion leads to mitochondrial glutamate trapping and malate-aspartate shuttle (MAS) dysfunction. C_LIO_LIRestoration of MAS activity in Glud1 deficient MuSCs reverses precocious differentiation and imbalanced fusion. C_LI

cell biology↗

bioRxiv2023

Toxin-mediated depletion of nicotinamide dinucleotides drives persister formation in a human pathogen

Toxin-antitoxin (TA) systems are widespread in bacteria and are implicated in genome stability, virulence, phage defense and persistence. Although TA systems encompass a large variety of molecular activities and cellular targets, their physiological role and regulatory mechanisms are often unclear1,2. Here, we show that a RES domain TA system increases the survival of the human pathogen P. aeruginosa during antibiotic treatment by generating a subpopulation of highly drug-tolerant persisters. The NatT toxin is an NAD phosphorylase, which leads to strong depletion of NAD and NADP in a subpopulation of cells. Actively growing P. aeruginosa cells effectively compensate for toxin-mediated NAD deficiency by inducing the NAD salvage path-way. In contrast, under nutrient-limited conditions, NatT generates NAD-depleted cells that give rise to drug tolerant persisters during outgrowth. Structural and biochemical analyses of active and inactive NatR-NatT complexes reveal how changes in NatR-NatT interaction controls toxin activity and autoregulation. Finally, we show that the NAD precursor nicotinamide blocks NatT activity and eliminates persister formation, exposing powerful metabolic feedback control of toxin activity. The findings that patient isolates contain natT gain-of-function alleles and that NatT increases P. aeruginosa virulence, argue that NatT contributes to P. aeruginosa fitness during infections. These studies provide mechanistic insight into how a TA system promotes pathogen persistence by disrupting essential metabolic pathways during nutrient stress.

microbiology↗

bioRxiv2023

De novo serine biosynthesis is protective in mitochondrial disease

Importance of serine as a metabolic regulator is well known in tumors and raising attention also in degenerative diseases. Recent data indicate that de novo serine biosynthesis is an integral component of metabolic response to mitochondrial disease, but the roles of the response have remained unknown. Here, we report that glucose-driven de novo serine biosynthesis maintains metabolic homeostasis in energetic stress. Pharmacological inhibition of the rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), aggravated mitochondrial muscle disease, suppressed oxidative phosphorylation and mitochondrial translation, altered whole-cell lipid profiles and enhanced mitochondrial integrated stress response (ISRmt), in vivo, in skeletal muscle and in cultured cells. Our evidence indicates that de novo serine biosynthesis is essential to maintain mitochondrial respiration, redox balance, and cellular lipid homeostasis in skeletal muscle with mitochondrial dysfunction. Our evidence implies that interventions activating de novo serine synthesis may protect against mitochondrial failure in the skeletal muscle. Bullet pointsO_LISerine becomes an essential amino acid in mitochondrial translation defects C_LIO_LIBlocking de novo serine biosynthesis promotes progression of mitochondrial disease C_LIO_LIDe novo serine biosynthesis maintains phospholipid homeostasis upon mitochondrial insult C_LIO_LISerine biosynthesis sustains redox-balance and mitochondrial translation in disease C_LI

cell biology↗

bioRxiv2023

A non-canonical function of LDHB promotes SLC7A11-mediated glutathione metabolism and protects against glutaminolysis-dependent ferroptosis in KRAS-driven lung cancer

Ferroptosis, a form of non-apoptotic cell death program driven by excessive lipid peroxidation and an important mechanism of tumor suppression, is frequently dysregulated in cancer. However, the mechanisms underlying impaired ferroptosis in oncogene-specific tumors remain poorly understood. Here we report a non- canonical role of lactate dehydrogenase B (LDHB), whose main activity is the conversion of lactate to pyruvate, in protecting KRAS-mutated lung cancer from ferroptosis. Silencing of LDHB impairs intracellular glutathione (GSH) metabolism and drives the hypersensitivity of KRAS-mutant cells to ferroptosis inducers by inhibiting the SLC7A11/GSH/GPX4 axis, a central antioxidant system against lipid peroxidation and ferroptosis by catalyzing GSH synthesis and utilization. Mechanistically, LDHB promotes SLC7A11 expression and GSH biosynthesis, and inhibition of LDHB confers metabolic synthetic lethality with ferroptosis inducers due to increased glutaminolysis and production of reactive oxygen species (ROS) in mitochondria, ultimately triggering ferroptosis of KRAS-driven lung cancer cells. Consequently, combined inhibition of LDHB and SLC7A11 synergistically suppresses tumor growth in multiple KRAS-mutant lung cancer implants and in an autochthonous model of Kras-induced lung adenocarcinoma. Taken together, our results reveal a hitherto unrecognized mechanism of ferroptosis defense by glycolytic LDHB and suggest a new strategy for the treatment of KRAS-dependent lung cancer.

cancer biology↗

bioRxiv2022

ROS induction as a strategy to target persister cancer cells with low metabolic activity in NRAS mutated melanoma

Metabolic reprogramming is an emerging hallmark of resistance to cancer therapy but may generate vulnerabilities that can be targeted with small molecules. Multi-omics analysis revealed that NRAS-mutated melanoma cells with a mesenchymal transcriptional profile adopt a quiescent metabolic program to resist cellular stress response induced by MEK-inhibitor resistance. However, as a result of elevated baseline ROS levels, these cells become highly sensitive to ROS induction. In vivo xenograft experiments and single-cell RNA sequencing demonstrated that intra-tumor heterogeneity requires the combination of a ROS-inducer and a MEK-inhibitor to target both tumor growth and metastasis. By ex vivo pharmacoscopy of 62 human metastatic melanomas, we found that MEK-inhibitor resistant tumors significantly benefitted from the combination therapy. Finally, we profiled 486 cancer cell lines and revealed that oxidative stress responses and translational suppression are biomarkers of ROS-inducer sensitivity, independent of cancer indication. These findings link transcriptional plasticity to a metabolic phenotype that can be inhibited by ROS-inducers in melanoma and other cancers. Statement of SignificanceTargeted-therapy resistance in cancer arises from genetic selection and both transcriptional and metabolic adaptation. We show that metabolic reprogramming sensitizes resistant cells to ROS-induction in combination with pathway inhibitors. Predictive biomarkers of metabolic sensitivity to ROS-inducing agents were identified in many cancer entities, highlighting the generalizability of this treatment approach. Graphical summary O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cancer biology↗

bioRxiv2022

Mitochondrial pyruvate metabolism regulates the activation of quiescent adult neural stem cells

Cellular metabolism is important for adult neural stem/progenitor cell (NSPC) behavior. However, its role in the transition from quiescence to proliferation is not fully understood. We here show that the mitochondrial pyruvate carrier (MPC) plays a crucial and unexpected part in this process. MPC transports pyruvate into mitochondria, linking cytosolic glycolysis to mitochondrial tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS). Despite its metabolic key function, the role of MPC in NSPCs has not been addressed. We show that quiescent NSPCs have an active mitochondrial metabolism and express high levels of MPC. Pharmacological MPC inhibition increases aspartate and triggers NSPC activation. Furthermore, genetic MPC-ablation in vivo also activates NSPCs, which differentiate into mature neurons, leading to overall increased hippocampal neurogenesis in adult and aged mice. These findings highlight the importance of metabolism for NSPC regulation and identify a novel pathway through which mitochondrial pyruvate import controls NSPC quiescence and activation. Highlights* Quiescent NSPCs have high levels of MPC and an active mitochondrial network * The import of pyruvate into mitochondria is necessary to maintain quiescence of NSPCs * MPC inhibition increases intracellular aspartate levels and triggers the activation of quiescent NSPCs * MPC-knockout NSPCs generate mature newborn neurons, leading to overall increased neurogenesis in adult and advanced age mice Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/494137v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1ee8788org.highwire.dtl.DTLVardef@1040633org.highwire.dtl.DTLVardef@1330d26org.highwire.dtl.DTLVardef@a474e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Structure of the connexin-43 gap junction channel reveals a closed sieve-like molecular gate

Gap junction channels (GJCs) mediate intercellular communication by connecting two neighboring cells and enabling direct exchange of ions and small molecules. Cell coupling via connexin-43 (Cx43) GJCs is important in a wide range of cellular processes in health and disease 1-3, yet the structural basis of Cx43 function and regulation has not been determined until now. Here we describe the structure of a human Cx43 GJC solved by cryo-EM and single particle analysis at 2.26 [A] resolution. The pore region of Cx43 GJC features several lipid-like densities per Cx43 monomer, located close to a putative lateral access site at the monomer boundary. We found a previously undescribed conformation on the cytosolic side of the pore, formed by the N-terminal domain and the transmembrane helix 2 of Cx43 and stabilized by a small molecule. Structures of the Cx43 GJC and hemichannels in nanodiscs reveal a similar gate arrangement. The features of the Cx43 GJC and hemichannel cryo-EM maps and the channel properties revealed by molecular dynamics simulations suggest that the captured states of Cx43 are consistent with a closed state.

biochemistry↗

bioRxiv2021

Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions

Seventy years following the discovery of peroxisomes, their proteome remains undefined. Uncovering the complete peroxisomal proteome, the peroxi-ome, is crucial for understanding peroxisomal activities and cellular metabolism. We used high-content microscopy to uncover the peroxi-ome of the model eukaryote - Saccharomyces cerevisiae. This strategy enabled us to expand the known organellar proteome by [~]40% and paved the way for performing systematic, whole-organellar proteome assays. Coupled with targeted experiments this allowed us to discover new peroxisomal functions. By characterizing the sub-organellar localization and protein targeting dependencies into the organelle, we unveiled non-canonical targeting routes. Metabolomic analysis of the peroxi-ome revealed the role of several newly-identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.

cell biology↗

bioRxiv2021

Epithelial-mesenchymal transition is the main driver of intrinsic metabolism in cancer cell lines

A fundamental feature of cancer cells is genomic heterogeneity. It is a main driver of phenotypic differences, including the response to drugs, and therefore a key factor in therapy selection. Motivated by the increasing role attributed to metabolic reprogramming in tumor development, we wondered how genomic heterogeneity affects metabolic phenotype. To this end, we profiled the intracellular metabolome of 180 cancer cell lines grown in similar conditions to exclude environmental factors. For each cell line, we estimate activity for 49 pathways across the whole metabolic network. Upon clustering of activity data, we found a convergence into only two major metabolic types. These were further characterized by 13C-flux analysis, lipidomics, and analysis of sensitivity to perturbations. These experiments revealed differences in lipid, mitochondrial, and carbohydrate metabolism between the two major types. Finally, a thorough integration of our metabolic data with multiple omics data revealed a strong association with markers of epithelial-mesenchymal transition (EMT). Our analysis indicates that in absence of variations imposed by the microenvironment, the metabolism of cancer cell lines falls into only two major classes despite genetic heterogeneity.

systems biology↗

bioRxiv2021

MSNovelist: De novo structure generation from mass spectra

Structural elucidation of small molecules de novo from mass spectra is a longstanding, yet unsolved problem. Current methods rely on finding some similarity with spectra of known compounds deposited in spectral libraries, but do not solve the problem of predicting structures for novel or poorly represented compound classes. We present MSNovelist that combines fingerprint prediction with an encoder-decoder neural network to generate structures de novo from fragment spectra. In evaluation, MSNovelist correctly reproduced 61% of database annotations for a GNPS reference dataset. In a bryophyte MS2 dataset, our de novo structure prediction substantially outscored the best database candidate for seven features, and a potential novel natural product with a flavonoid core was identified. MSNovelist allows predicting structures solely from MS2 data, and is therefore ideally suited to complement library-based annotation in the case of poorly represented analyte classes and novel compounds.

bioinformatics↗