Lloyd M. Smith

Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry

This paper introduces RaPiD-mAb-MS, a direct infusion mass spectrometry method for rapid peptide mapping of monoclonal antibodies, achieving 100-fold faster analysis with high sequence coverage and comparable results to conventional methods.

DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation

This study shows DNA damage induces alternative splicing of RIF1, generating isoforms that affect DNA repair complex assembly and phase separation.

Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia

The paper identifies BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia by analyzing interactome changes in mutant UBQLN2 proteins.

Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues

This study develops a chemoselective method to profile newly synthesized extracellular matrix proteins in bioengineered tumor tissues, revealing distinct ECM synthesis patterns in response to different extracellular environments.

Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation

The paper introduces PIP-ECHO, a method to control false discovery rate in peptide-identity-propagation, showing it outperforms existing tools in FDR control and differential protein abundance detection.

Discovery of dehydroamino acids and their crosslinks in Tau and other aggregating proteins of Alzheimers disease

This study identifies dehydroamino acids and their crosslinks in Alzheimer's disease brain proteome, showing increased prevalence in AD compared to controls.

IsoBayes: a Bayesian approach for single-isoform proteomics inference

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs

The paper identifies RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs, revealing new host factors involved in viral replication and antiviral defense.

Axon guidance pathways modulate neurotoxicity of ALS-associated UBQLN2

This study identifies axon guidance pathways as modulators of UBQLN2 toxicity in ALS/FTD, showing reduced neurodegeneration with UNC5B and DCC suppression in multiple models.

Fused in sarcoma regulates DNA replication timing and progression

This study identifies FUS's role in DNA replication timing and progression, showing its importance in genome stability and its potential contribution to disease.

Automated Assignment of Proteoform Classification Levels

The paper implements a five-level proteoform classification system in MetaMorpheus and develops a stand-alone tool to classify proteoform identifications from any software that provides sufficient ambiguity information.

O-Pair Search with MetaMorpheus for O-glycopeptide Characterization

O-Pair Search identifies O-glycopeptides and localizes O-glycosites using collision- and electron-based dissociation spectra, improving speed and identification rates.

Spritz: A Proteogenomic Database Engine

Spritz generates sample-specific proteogenomic databases annotated with sequence variations and PTMs from RNA-seq data, enabling improved identification of proteoforms in mass spectrometry analyses.

Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the Galaxy Platform.

The paper evaluates and implements two label-free quantification tools in the Galaxy platform for proteomics and multi-omics analysis.