Biology subjects

Dawson, S. L.

Publications and source records attributed to Dawson, S. L..

3 recordsLinked to original sources

bioRxiv2025

Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein Interactions, and Disease Biomarkers with High Throughput

The GoDig platform enables sensitive, multiplexed targeted pathway proteomics without manual scheduling or synthetic standards. Here we present GoDig 2.0, which increases sample multiplexing to 35-fold, improves time efficiency and reduces scan delays for higher success rates, and allows flexible spectral and elution library generation from different mass spectrometry data types. GoDig 2.0 measures 2.4x more targets than GoDig 1.0, quantifying >99% of 800 peptides in a single run. We compiled a library of 23,989 human phosphorylation sites from a phosphoproteomic dataset and used it to profile kinase signaling differences across cell lines. In human brain tissue, we established a hyperphosphorylated tau assay including pTau127, revealing potential biomarkers for Alzheimers disease. We also quantified diglycyl-lysine peptides to assess polyubiquitin branching. Finally, we built a library of 20,946 reactive cysteines and profiled covalent compound-protein interactions spanning diverse pathways. GoDig 2.0 enables high-throughput analyses of site-specific protein modifications across many biological contexts.

biochemistry↗

bioRxiv2024

Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer

Comprehensive global proteome profiling that is amenable to high throughput processing will broaden our understanding of complex biological systems. Here, we evaluated two leading mass spectrometry techniques, Data Independent Acquisition (DIA) and Tandem Mass Tagging (TMT), for extensive protein abundance profiling. DIA provides label-free quantification with a broad dynamic range, while TMT enables multiplexed analysis using isobaric tags for efficient cross-sample comparisons. We analyzed 18 samples, including four cell lines (IHCF, HCT116, HeLa, MCF7) under standard growth conditions, in addition to IHCF treated with two H2O2 concentrations, all in triplicate. Experiments were conducted on an Orbitrap Astral mass spectrometer, employing Field Asymmetric Ion Mobility Spectrometry (FAIMS). Despite utilizing different acquisition strategies, both the DIA and TMT approaches achieved comparable proteome depth and quantitative consistency, with each method quantifying over 10,000 proteins across all samples, with slightly more protein-level precision for the TMT strategy. Relative abundance correlation analysis showed strong agreement at both peptide and protein levels. Our findings highlight the complementary strengths of DIA and TMT for high-coverage proteomic studies, providing flexibility in method selection based on specific experimental needs.

biochemistry↗

bioRxiv2024

Associations between oral microbiota pathogens and elevated depressive and anxiety symptoms in men

BackgroundSystemic inflammation has been associated with depression. Certain oral bacterial species contribute to extra oral inflammation, however their potential association with mental disorders remains unclear. This study investigated the associations between oral microbiota pathogens and depressive and anxiety symptoms. MethodsData came from 436 men from the Geelong Osteoporosis Study. Using 16S rRNA gene sequencing, we characterized the oral microbiota composition and created a composite variable representing the prevalence of known oral pathogens, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatum, and Prevotella nigrescens. Binary variables were created representing elevated depressive and anxiety symptoms using the Hospital Anxiety and Depression Scale. Associations between oral pathogens and elevated depressive/anxiety symptoms were analyzed using logistic regression adjusted for confounders (age, socio-economic status, diet, smoking, alcohol, exercise, obesity and hypertension). ResultsWe found limited evidence for an association between the pathogen composite and elevated depressive (N = 39) but not anxiety (N = 66) symptoms. Moreover, some of the comprising species, P. nigrescens (OR 1.61 (95% CI 1.21, 2.13)) and F. nucleatum (subsp. animalis ATCC 51191 (1.54 (1.13, 2.11)), subsp. animalis (1.47 (1.05, 2.08)) and subsp. vincentii (1.47 (1.06, 2.04))) were associated with elevated depressive symptoms. Exploratory analyses revealed several other taxa associated with depression and anxiety. LimitationsThis study focuses on mental health symptoms and not diagnoses in men, and the results may not be generalizable to women. ConclusionsWe identified several taxa within the oral microbiota that were associated with depressive and anxiety symptoms. Further replication and mechanistic studies are needed. HighlightsO_LIA composite of oral pathogens is associated with depressive symptoms in adult men C_LIO_LIAssociations between P. nigrescens and other species and elevated depressive symptoms C_LIO_LIAssociations remain following adjustment for confounders C_LIO_LIOral microbial diversity was not associated with depressive or anxiety symptoms C_LIO_LIFewer associations between oral microbial composition and anxiety than depression C_LI

microbiology↗