Biology subjects

Sing, J. C.

Publications and source records attributed to Sing, J. C..

3 recordsLinked to original sources

bioRxiv2026

STRIDE: Signal Transfer and Aligned Ion-Peak Discrimination for Peptidoform Evidence for Consistent Quantification of Site-Localized Post-Translational Modifications in Large-Scale DIA-MS

Data-independent acquisition (DIA) mass spectrometry has emerged as a powerful method for comprehensive post-translational modification profiling in proteomics, but faces challenges in consistently assigning peptidoforms to the same chromatographic peaks across multiple samples. This study introduces STRIDE to address this challenge by implementing dynamic programming alignment and propagating unique ion signature signals across runs. We benchmarked STRIDE using a synthetic phosphopeptide dilution series dataset, demonstrating an 11.3-fold reduction in false-negative rate compared to DIA-NN, from 68% with DIA-NN to 6% with STRIDE at 5% false-positive rate when requiring both correct site-localization and correct peak assignment. STRIDE also improved over the base OpenSWATH (IPF), reducing the false-negative rate from 14% to 6% for correct peak assignment. When applied to a phospho-enriched U2OS nocodazole dataset, our approach reduced missing values from 38.6% to 15.2% in a representative quantification matrix, increased highly reproducible phosphopeptide detections from 7,698 to 12,510 in nocodazole-treated samples, and identified 5,431 differentially abundant phosphopeptides compared to 2,588 with DIA-NN. This increased the number of enriched pathways recovered from differential phosphopeptide analysis, including pathways related to mitotic arrest, microtubule organization, chromatin regulation, RNA processing and kinase signalling. Lastly, we analyzed acetyllysine and glycopeptide-enriched DIA datasets, where STRIDE improved complete replicate detection, reduced missing quantification values, and increased site-specific glycan reproducibility. Together, these results demonstrate that STRIDE improves peptidoform proteomics through reduced false-negative rates, consistent peak assignment, and more complete quantification across runs.

bioinformatics↗

bioRxiv2024

MassDash: A Web-based Dashboard for Targeted Mass Spectrometry Visualization

With the increased usage, diversity of methods and instruments being applied to analyze Data-Independent Acquisition (DIA) data, visualization is becoming increasingly important to validate automated software results. Here we present MassDash, a cross-platform, DIA mass spectrometry visualization and validation software for comparing features and results across popular tools. MassDash provides a web-based interface and Python package for interactive feature visualizations and summary report plots across multiple automated DIA feature detection tools including OpenSwath, DIA-NN, and dreamDIA. Furthermore, MassDash processes peptides on the fly, enabling interactive visualization of peptides across dozens of runs simultaneously on a personal computer. MassDash supports various multidimensional visualizations across retention time, ion mobility, m/z, and intensity providing additional insights into the data. The modular framework is easily extendable enabling rapid algorithm development of novel peak picker techniques, such as deep learning based approaches and refinement of existing tools. MassDash is open-source under a BSD 3-Clause license and freely available at https://github.com/Roestlab/massdash, and a demo version can be accessed at https://massdash.streamlit.app.

bioinformatics↗

bioRxiv2023

Diagnostic Potential of Shallow Depth Gut Metagenomics Sequencing for Atherosclerotic Cardiovascular Disease Risk Stratification

BackgroundCardiovascular disease, specifically atherosclerotic cardiovascular disease (ACVD), presents a burden on society in terms of financial resources and quality of life that is only expected to grow in the coming years. Current diagnostic methods lack the sensitivity or specificity to confidently screen for atherosclerotic cardiovascular disease and are either costly, invasive, or both. Building on previous research linking ACVD to changes in the microbiome, we hypothesized that one could build a machine learning classifier for ACVD that makes use of shallow depth microbiome data. Methods and FindingsRaw metagenomics Illumina paired end sequencing data was downloaded from the European Bioinformatics Institute (EBI) public database under accession ERP023788. The dataset includes 383 Han Chinese subjects of which 170 are control subjects and 214 are ACVD subjects. The raw sequencing data was subsampled using seqtk to generate in silico shallow depth datasets at various depths. Each subsampled experiment was processed through KneadData for quality control, and finally relative abundances were acquired through Kraken2. Based on in-silico down sampling experiments, we demonstrate that species level information is still captured at read depths as low as 50K reads per sample, consistent with current literature. In addition, the shallow depth data (50K) contains relevant taxa information for stratification of ACVD patients. Differential expression analysis identified a variety of Streptococcus species and Escherichia coli enriched in ACVD patients and a few low abundance Bacteroides species in ACVD patients, which have been previously reported. ConclusionHere, using publicly available data, we show with in silico experiments that species-level microbiome information is preserved at low sequencing depths that would allow a screening or diagnostic tool to be cost-competitive with currently used methods such as stress ECGs and stress ECHO tests. Additionally, we show that we can indeed make a microbiome-based model with performance metrics comparable to or better than front-line or mid-tier tests.

bioinformatics↗