Deanna L. Plubell

Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition

This study revisits resonance-excitation collision-induced dissociation (reCID) for DIA proteomics, showing it can achieve performance comparable to HCD with optimized settings and libraries.

Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies

This study compares the effects of two IL-6 inhibitors on serum extracellular vesicles using proteomics, finding distinct protein pathway alterations.

Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer

The paper develops scalable targeted proteomics assays using the Stellar mass spectrometer for analyzing biofluids, demonstrating high sensitivity and multiplexing capabilities.

Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists

This paper evaluates a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics, showing improved performance in ion detection and quantitative precision compared to the standard Orbitrap Astral MS.

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer

The paper demonstrates using data-independent acquisition (DIA) to select peptides for targeted proteomics assays, achieving comparable quantitative precision to existing methods.

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle:High-Resolution Sampling Every 4 Hours Over 22 Days

The paper describes a high-resolution microbial metagenome dataset collected over 22 days during a phytoplankton bloom cycle, including gene abundances and time-matched environmental data.

A framework for quality control in quantitative proteomics

The paper introduces a framework for quality control in quantitative proteomics, combining internal and external QC measures with tools for data analysis and deposition.

A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease

The paper presents a high-quality quantitative proteomics dataset for Alzheimer's disease, including samples from different brain regions and clinical groups.

Proteomics of resilience to Alzheimer's disease identifies brain regional soluble Aβ levels, actin filament processes, and response to injury

The paper identifies proteomic features of resilience to Alzheimer's disease, finding lower soluble Aβ levels and specific protein interactions in brain regions associated with resistance to dementia.

Improving power while controlling the false discovery rate when only a subset of peptides are relevant

The paper introduces a new method to control the false discovery rate in proteomics when only a subset of peptides are relevant, showing it outperforms existing methods.

Genetic control of the HDL proteome

The paper identifies genetic regulation of HDL proteome variation across mouse strains, revealing coordinated protein regulation and functional diversity in HDL subspecies.