Lloyd M. Smith
YOU?
Author Swipe
View article: Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia
Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia Open
Ubiquilin-2 (UBQLN2) is a ubiquitin (Ub)-binding shuttle protein that is mutated in X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS/FTD-linked mutations in UBQLN2 disrupt its conformation, incre…
View article: Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues
Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues Open
In both native and engineered tissues, the extracellular matrix (ECM) supports and regulates nearly all aspects of cellular pathophysiology, and in response, cells extensively remodel their surrounding extracellular environments through ne…
View article: Identifying lncRNA–Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry
Identifying lncRNA–Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry Open
Long noncoding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure and function of these complexes …
View article: IsoBayes: a Bayesian approach for single-isoform proteomics inference
IsoBayes: a Bayesian approach for single-isoform proteomics inference Open
Motivation Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly…
View article: Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation
Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation Open
The goal of proteomics is to identify and quantify peptides and proteins within a biological sample. Almost all algorithms for the identification of peptides in LC-MS/MS data employ two steps: peptide/spectrum matching and peptide-identity…
View article: A Fast Neural Network for Isotopic Charge State Assignment
A Fast Neural Network for Isotopic Charge State Assignment Open
Electrospray ionization (ESI) mass spectrometry is an essential technique for chemical analysis in a range of fields. In ESI, analytes can produce multiple charge states, which must be correctly assigned for identification. Existing approa…
View article: Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues
Chemoselective Characterization of New Extracellular Matrix Deposition in Bioengineered Tumor Tissues Open
The extracellular matrix (ECM), present in nearly all tissues, provides extensive support to resident cells through structural, biomechanical, and biochemical means, and in return the ECM undergoes constant remodeling from interacting cell…
View article: Directed Evolution of APOX for Proximity Labeling Using Phenols with High Redox Potentials
Directed Evolution of APOX for Proximity Labeling Using Phenols with High Redox Potentials Open
Proximity labeling (PL) identifies endogenous proteins in specific subcellular regions. APEX2 is a peroxidase that enables PL with high temporal resolution by oxidizing biotin phenol (BP) into a radical that tags nearby proteins. However, …
View article: A Fast Neural Network for Isotopic Charge State Assignment
A Fast Neural Network for Isotopic Charge State Assignment Open
Electrospray ionization (ESI) mass spectrometry is an essential technique for chemical analysis in a range of fields. In ESI, analytes can produce multiple charge states, which must be correctly assigned for identification. Existing approa…
View article: Dehydroamino acids and their crosslinks in Alzheimer’s disease aggregates
Dehydroamino acids and their crosslinks in Alzheimer’s disease aggregates Open
Alzheimer’s disease (AD) is characterized by the accumulation of protein aggregates, which are thought to be influenced by posttranslational modifications (PTMs). Dehydroamino acids (DHAAs) are rarely observed PTMs that contain an electrop…
View article: Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation
Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation Open
The goal of proteomics is to identify and quantify peptides and proteins within a biological sample. Almost all algorithms for the identification of peptides in LC-MS/MS data employ two steps: peptide/spectrum matching and peptide-identity…
View article: DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation
DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation Open
How RIF1 (RAP1 interacting factor) fulfills its diverse roles in DNA double-strand break (DSB) repair, DNA replication, and nuclear organization remains elusive. Here we show that alternative splicing (AS) of a cassette exon (Ex32) encodin…
View article: Identification of Host Proteins Involved in Hepatitis B Virus Genome Packaging
Identification of Host Proteins Involved in Hepatitis B Virus Genome Packaging Open
A critical part of the hepatitis B virus (HBV) life cycle is the packaging of the pregenomic RNA (pgRNA) into nucleocapsids. While this process is known to involve several viral elements, much less is known about the identities and roles o…
View article: <i>IsoBayes</i> : a Bayesian approach for single-isoform proteomics inference
<i>IsoBayes</i> : a Bayesian approach for single-isoform proteomics inference Open
Motivation Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly…
View article: Spectral averaging with outlier rejection algorithms to increase identifications in top‐down proteomics
Spectral averaging with outlier rejection algorithms to increase identifications in top‐down proteomics Open
The identification of proteoforms by top‐down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may inclu…
View article: Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs
Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs Open
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate differe…
View article: Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue
Cysteine Counting via Isotopic Chemical Labeling for Intact Mass Proteoform Identifications in Tissue Open
Top-down proteomics, the tandem mass spectrometric analysis of intact proteoforms, is the dominant method for proteoform characterization in complex mixtures. While this strategy produces detailed molecular information, it also requires ex…
View article: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs
Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs Open
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate…
View article: Newly synthesized glycoprotein profiling to identify molecular signatures of warm ischemic injury in donor lungs
Newly synthesized glycoprotein profiling to identify molecular signatures of warm ischemic injury in donor lungs Open
This study developed and implemented a bioorthogonal strategy to chemoselectively label, enrich, and characterize newly synthesized (NewS-)glycoproteins during 4-h ex vivo lung perfusion (EVLP). Through this approach, the investigators unc…
View article: Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue
Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue Open
RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein …
View article: Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2
Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2 Open
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2 ) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated …
View article: The Human Proteoform Project: Defining the human proteome
The Human Proteoform Project: Defining the human proteome Open
Proteins are the primary effectors of function in biology, and thus, complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is exp…
View article: Artificial mismatch hybridization
Artificial mismatch hybridization Open
An improved nucleic acid hybridization process is provided which employs a modified oligonucleotide and improves the ability to discriminate a control nucleic acid target from a variant nucleic acid target containing a sequence variation. …
View article: Overview and considerations in bottom-up proteomics
Overview and considerations in bottom-up proteomics Open
This review provides a broad overview of mass spectrometry-based proteomics and highlights four developing areas: (1) protein inference, (2) alternative proteases, (3) sample-specific databases and (4) post-translational modification disco…