Samuel Payne
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View article: CMC Arthroplasty for Treatment of the Painful and Arthritic Thumb: A Review of Surgical Treatment Options with Preferred Technique
CMC Arthroplasty for Treatment of the Painful and Arthritic Thumb: A Review of Surgical Treatment Options with Preferred Technique Open
Arthritis of the first carpometacarpal joint is a prevalent and often disabling condition for many older adults. The diagnosis is typically established through a comprehensive patient history, physical examination, and confirmatory radiogr…
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: Activating Cancer Hallmarks through Changes in mRNA/Protein Regulation
Activating Cancer Hallmarks through Changes in mRNA/Protein Regulation Open
As a diverse family of diseases, cancer is unified by a set of common dysfunctions, such as limitless growth potential and an insensitivity to antigrowth signals. These shared overarching biological processes have been termed the hallmarks…
View article: Ramp Sequence May Explain Synonymous Variant Association with Alzheimer’s Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA)
Ramp Sequence May Explain Synonymous Variant Association with Alzheimer’s Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) Open
Background: The synonymous variant NC_000007.14:g.100373690T>C (rs2405442:T>C) in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) gene was previously associated with decreased risk for Alzheimer’s disease (AD) in genome-wide a…
View article: Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence Open
Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new c…
View article: Ramp sequence may explain synonymous variant association with Alzheimer’s disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (<i>PILRA</i>)
Ramp sequence may explain synonymous variant association with Alzheimer’s disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (<i>PILRA</i>) Open
BACKGROUND Synonymous variant NC_000007.14:g.100373690T>C ( rs2405442:T>C ) in the Paired Immunoglobulin-like Type 2 Receptor Alpha ( PILRA ) gene was previously associated with decreased risk for Alzheimer’s disease (AD) in genome-wide as…
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: Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation
Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation Open
Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in b…
View article: Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses
Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses Open
Single-cell analysis is an active area of research in many fields of biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information to sample averages. Many…
View article: Comprehensive proteogenomic characterization of rare kidney tumors
Comprehensive proteogenomic characterization of rare kidney tumors Open
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immu…
View article: Pushing the Isotopic Envelope: When carrier channels pollute their neighbors’ signals
Pushing the Isotopic Envelope: When carrier channels pollute their neighbors’ signals Open
Individual cells are the foundational unit of biology, and understanding their functions and interactions is critical to advancing our understanding of health and disease. Single cell proteomics has seen intense interest from mass spectrom…
View article: Human tear film protein sampling using soft contact lenses
Human tear film protein sampling using soft contact lenses Open
Background Human tear protein biomarkers are useful for detecting ocular and systemic diseases. Unfortunately, existing tear film sampling methods (Schirmer strip; SS and microcapillary tube; MCT) have significant drawbacks, such as pain, …
View article: TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis
TDP-43-stratified single-cell proteomics of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis Open
A limitation of conventional bulk-tissue proteome studies in amyotrophic lateral sclerosis (ALS) is the confounding of motor neuron (MN) signals by admixed non-MN proteins. Here, we leverage laser capture microdissection and nanoPOTS singl…
View article: Unscheduled Healthcare Contact after Outpatient Surgical Fixation of Distal Radius Fractures: A Retrospective Cohort Study
Unscheduled Healthcare Contact after Outpatient Surgical Fixation of Distal Radius Fractures: A Retrospective Cohort Study Open
Background: Distal radius fractures (DRFs) commonly require surgical fixation. Unscheduled healthcare contact (UHC) after surgery represents an area of quality improvement in surgical care. We hypothesize that UHC after outpatient surgical…
View article: Evaluating a large language model’s ability to solve programming exercises from an introductory bioinformatics course
Evaluating a large language model’s ability to solve programming exercises from an introductory bioinformatics course Open
Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and resear…
View article: Proteogenomic data and resources for pan-cancer analysis
Proteogenomic data and resources for pan-cancer analysis Open
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitat…
View article: Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation
Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation Open
Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in b…
View article: Data‐Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label‐Free Single‐Cell Proteomics**
Data‐Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label‐Free Single‐Cell Proteomics** Open
We combined efficient sample preparation and ultra‐low‐flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label…
View article: Data‐Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label‐Free Single‐Cell Proteomics**
Data‐Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label‐Free Single‐Cell Proteomics** Open
We combined efficient sample preparation and ultra‐low‐flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label…
View article: TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis
TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis Open
Summary Unbiased proteomics has been employed to interrogate central nervous system (CNS) tissues (brain, spinal cord) and fluid matrices (CSF, plasma) from amyotrophic lateral sclerosis (ALS) patients; yet, a limitation of conventional bu…
View article: Discovery and Detection of Dry Eye Disease Protein Biomarkers Using Soft Contact Lens Tear Sampling
Discovery and Detection of Dry Eye Disease Protein Biomarkers Using Soft Contact Lens Tear Sampling Open
Dry eye disease (DED) affects up to half of the world’s population and causes blur, eye pain, decreased quality of life. Unfortunately, many people do not receive proper treatment due to current challenges associated with DED diagnoses. To…