Biology subjects

Cantrell, L. S.

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

8 recordsLinked to original sources

bioRxiv2026

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics

Modern DIA proteomics increasingly emphasizes throughput and depth for large-cohort studies, but methods are often optimized using proxy metrics that can mask losses in quantifiable signal and statistical power. Here, we evaluate how datapoints per peak and other chromatographic features jointly contribute to quantification and downstream biological discovery. Using a matrix-matched calibration curve dataset, we checked how the number of datapoints per peak (DPPP) affects the limits of detection and quantification (LOD/LOQ). Reduced DPPP minimally affected LOD but substantially degraded LOQ. Feature modeling and nonparametric association analyses identified precursor peak area as the strongest feature-level predictor of LOQ, whereas DPPP showed weaker and context-dependent effects. Simulations of chromatographic peak integration recapitulated these trends, showing that increased sampling primarily improves integration precision, while quantitative accuracy is strongly governed by peak height and peak shape. Finally, when comparing 20 cancer vs 20 control plasma samples processed with Seer Proteograph, the decrease in DPPP led to a loss of statistical significance for proteins with low-abundance precursors. These findings argue that DIA optimization should prioritize LOQ and statistical power metrics - not identifications alone - by balancing sampling density with chromatographic peak height and quality to maximize useful biological signal.

bioinformatics↗

bioRxiv2026

Radiant DIA: A Fast, Sensitive, and Accurate Search Engine for Quantitative Proteomics

In mass spectrometry-based proteomics, robust and efficient search engines are essential for accurate peptide and protein identification and quantification. Advances in sample preparation and instrumentation have increased the demand for highly scalable processing tools, with datasets comprising hundreds or thousands of samples in single-cell and population studies. Here we present Radiant DIA, a novel Data-Independent Acquisition search engine which achieves 4x faster processing and 10x lower cloud compute costs for large experiments while ensuring rigorous control of false discovery rate (FDR) and maintaining similar sensitivity, precision, and quantitative accuracy to widely-used tools. The Radiant DIA search engine is paired with a modular pipeline deployable on cloud and desktop environments comprising individual modules for distributed re-scoring, FDR estimation, protein inference and quantification. Unlike traditional monolithic applications, this architecture enables high-performance, cloud-scale analysis without sacrificing local usability. Together, the Radiant DIA and Fulcrum Pipeline tools enhance computational efficiency to facilitate biological discovery in large-scale proteomics, as demonstrated by analyses of real-world experiments up to thousands of MS acquisitions.

bioinformatics↗

bioRxiv2024

Cloud-enabled Scalable Analysis of Large Proteomics Cohorts

Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies are enabling large-scale cohort proteomic and proteogenomic analyses. As such studies scale, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in search engines that rely on library-free match between runs (MBR) search, which enable enhanced depth-per-sample and data completeness. However, to-date, no MBR-based search could scale to process cohorts of thousands or more individuals. Here, we present a strategy to deploy search engines in a distributed cloud environment without source code modification, thereby enhancing resource scalability and throughput. Additionally, we present an algorithm, Scalable MBR, that replicates the MBR procedure of the popular DIA-NN software for scalability to thousands of samples. We demonstrate that Scalable MBR can search thousands of MS raw files in a few hours compared to days required for the original DIA-NN MBR procedure and demonstrate that the results are almost indistinguishable to those of DIA-NN native MBR. The method has been tested to scale to over 15,000 injections and is available for use in the Proteograph Analysis Suite.

bioinformatics↗

bioRxiv2023

Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics

BackgroundThe wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic range of protein abundances into a mass spectrometry (MS)-accessible detection range. This enhances the depth and scalability of quantitative MS-based methods, which can elucidate the molecular mechanisms of biological processes, discover new protein biomarkers, and improve comprehensiveness of MS-based diagnostics. MethodsInvestigating multi-species spike-in experiments and a cohort, we investigated fold-change accuracy, linearity, precision, and statistical power for the using the Proteograph Product Suite, a deep plasma proteomics workflow, in conjunction with multiple MS instruments. ResultsWe show that NP-based workflows enable accurate identification (false discovery rate of 1%) of more than 6,000 proteins from plasma (Orbitrap Astral) and, compared to a gold standard neat plasma workflow that is limited to the detection of hundreds of plasma proteins, facilitate quantification of more proteins with accurate fold-changes, high linearity, and precision. Furthermore, we demonstrate high statistical power for the discovery of biomarkers in small- and large-scale cohorts. ConclusionsThe automated NP workflow enables high-throughput, deep, and quantitative plasma proteomics investigation with sufficient power to discover new biomarker signatures with a peptide level resolution.

biochemistry↗

bioRxiv2022

Proteome Remodeling of the Eye Lens at 50 Years Identified with Data-Independent Acquisition

The eye lens is responsible for focusing and transmitting light to the retina. The lens does this in the absence of organelles yet maintains transparency for at least five decades before onset of age-related nuclear cataract (ARNC). It is hypothesized that oxidative stress contributes significantly to ARNC formation. It is additionally hypothesized that transparency is maintained by a microcirculation system (MCS) that delivers antioxidants to the lens nucleus and exports small molecule waste. Common data-ependent acquisition (DDA) methods are hindered by dynamic range of lens protein expression and provide limited context to age-related changes in the lens. In this study we utilized data-independent acquisition (DIA) mass spectrometry to analyze the urea insoluble, membrane protein fractions of 16 human lenses subdivided into three spatially distinct lens regions to characterize age-related changes, particularly concerning the lens MCS and oxidative stress response. In this pilot cohort, we measured 4,788 distinct protein groups, 46,681 peptides, and 7,592 deamidated sequences, more than in any previous human lens DDA approach. Our results reveal age-related changes previously known in lens biology and expand on these findings, taking advantage of the rich dataset afforded by DIA. Principally, we demonstrate that a significant proteome remodeling event occurs at approximately 50 years of age, resulting in metabolic preference for anaerobic glycolysis established with organelle degradation, decreased abundance of protein networks involved in calcium-dependent cell-cell contacts while retaining networks related to oxidative stress response. Further, we identified multiple antioxidant transporter proteins not previously detected in the human lens and describe their spatiotemporal and age-related abundance changes. Finally, we demonstrate that aquaporin-5, among other proteins, is modified with age by PTMs including deamidation and truncation. We suggest that the continued accumulation of each of these age-related outcomes in proteome remodeling contribute to decreased fiber cell permeability and result in ARNC formation.

biochemistry↗

bioRxiv2022

Lens aquaporin-5 inserts into bovine fiber cell plasma membranes through mitochondria-associated lysosome secretion

PURPOSETo spatially map aquaporin-5 (AQP5) expression in bovine lens, molecularly characterize cytoplasmic AQP5-containing vesicles in the outer cortex, and elucidate AQP5 membrane trafficking mechanisms. METHODSImmunofluorescence was performed on bovine lens cryosections using AQP5, TOMM20, COX IV, calnexin, LC3B, LIMP-2, and connexin-50 antibodies and the fluorescent lipid membrane dye CM-DiI. AQP5 plasma membrane insertion was defined via line expression profile analysis. Transmission electron microscopy (TEM) was performed on bovine lens tissue sections to define cytoplasmic organelle identity, morphology, and subcellular localization in cortical fiber cells. Bovine lenses were treated with 10 nM bafilomycin A1 or 0.1% dimethyl sulfoxide vehicle control in ex vivo culture to determine changes in AQP5 plasma membrane expression. RESULTSImmunofluorescence analysis revealed cytoplasmic AQP5 expression in bovine lens epithelial cells and differentiating fiber cells. In the bovine lens cortex, complete AQP5 plasma membrane insertion occurs at r/a 0.951 + 0.005. AQP5-containing cytoplasmic vesicles are spheroidal, tubular in morphology, express TOMM20, and contain LC3B and LIMP-2 as fiber cells mature. TEM analysis revealed spheroidal, tubular autophagosomes, autolysosomes, and lysosomes with degrading mitochondria. AQP5-containing cytoplasmic vesicles and autolysosomes dock and fuse with the plasma membrane. Bafiloymcin A1 treatment reduced AQP5 plasma membrane expression by 27%. CONCLUSIONSAQP5 localizes to spheroidal, tubular cytoplasmic vesicles in the differentiating bovine lens fiber cells. During fiber cell differentiation, these vesicles incorporate LC3B and fuse with LIMP-2-positive lysosomes. AQP5 trafficking to the plasma membrane occurs through lysosome secretion as a novel mechanism of AQP5 trafficking.

cell biology↗

bioRxiv2021

Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging

The ocular lens proteome undergoes post-translational and progressive degradation as fiber cells age. The oldest fiber cells and the proteins therein are present at birth and are retained through death. Transparency of the lens is maintained in part by the high abundance crystallin family proteins (up to 300 mg/mL), which establishes a high dynamic range of protein abundance. As a result, previous Data Dependent Analysis (DDA) measurements of the lens proteome are less equipped to identify the lowest abundance proteins. In an attempt to probe more deeply into the lens proteome, we measured the insoluble lens proteome of an 18-year-old human with DDA and newer Data Independent Analysis (DIA) methods. By applying library free DIA search methods, 4,564 protein groups, 48,474 peptides and 5,577 deamidation sites were detected: significantly outperforming the quantity of identifications in using DDA and Pan-Human DIA library searches. Finally, by segmenting the lens into multiple fiber cell-age related regions, we uncovered cell-age resolved changes in proteome composition and putative function.

biochemistry↗

bioRxiv2021

Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies

Imaging mass spectrometry (IMS) allows the location and abundance of lipids to be mapped across tissue sections of human retina. For reproducible and accurate information, sample preparation methods need to be optimized. Paraformaldehyde fixation of a delicate multilayer structure like human retina facilitates the preservation of tissue morphology by forming methylene bridge cross-links between formaldehyde and amine/ thiols in biomolecules; however, retina sections analyzed by IMS are typically fresh-frozen. To determine if clinically significant inferences could be reliably based on fixed tissue, we evaluated the effect of fixation on analyte detection, spatial localization, and introduction of artefactual signals. Hence, we assessed the molecular identity of lipids generated by matrix-assisted laser desorption ionization (MALDI-IMS) and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) for fixed and fresh-frozen retina tissues in positive and negative ion modes. Based on MALDI-IMS analysis, more lipid signals were observed in fixed compared to fresh-frozen retina. More potassium adducts were observed in fresh-frozen tissues than fixed as the fixation process caused displacement of potassium adducts to protonated and sodiated species in ion positive ion mode. LC-MS/MS analysis revealed an overall decrease in lipid signals due to fixation that reduced glycerophospholipids and glycerolipids and conserved most sphingolipids and cholesteryl esters. The high quality and reproducible information from untargeted lipidomics analysis of fixed retina informs on all major lipid classes, similar to fresh-frozen retina, and serves as a steppingstone towards understanding of lipid alterations in retinal diseases.

biochemistry↗