Benjamin A. Neely
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View article: Retrieval-augmented generation for interpreting clinical laboratory regulations using large language models
Retrieval-augmented generation for interpreting clinical laboratory regulations using large language models Open
Large language models (LLMs) have demonstrated strong performance on general knowledge tasks, but they have important limitations as standalone tools for question answering in specialized domains where accuracy and consistency are critical…
View article: Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life
Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life Open
Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromo…
View article: Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government
Controlled environment agriculture: An opportunity to strengthen interagency research collaboration in the US government Open
Challenges facing food production and agricultural systems are increasingly interconnected with economic, security, health, and equity issues, among others. Threats such as extreme weather, economic volatility, and shrinking water resource…
View article: Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease
Proteomics Approaches to Ecoimmunology: New Insights into Wildlife Immunity and Disease Open
Synopsis Understanding wildlife immune responses is crucial for assessing disease risks, environmental stress effects, and conservation challenges. Traditional ecoimmunology approaches rely on targeted assays, which, while informative, oft…
View article: Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions
Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions Open
Domoic acid is a neurotoxin secreted by the marine diatom genus Pseudo-nitzschia during toxic algal bloom events. California sea lions (Zalophus californianus) are exposed to domoic acid through the ingestion of fish that fee…
View article: Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures Open
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-la…
View article: The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF Open
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats u…
View article: The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF Open
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats u…
View article: Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry Open
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins a…
View article: Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (<i>Zalophus californianus</i>)
Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (<i>Zalophus californianus</i>) Open
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis (DAT) have consistently increased. Outside of direct measurement of domoic acid in bodily fluids at the time of strandin…
View article: Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions
Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions Open
Domoic acid is a neurotoxin secreted by the marine diatom genus, Pseudo-nitzschia , during toxic algal bloom events. California sea lions ( Zalophus californianus ) are exposed to domoic acid through ingestion of fish that feed on toxic di…
View article: Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (<i>Zalophus californianus</i>)
Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions (<i>Zalophus californianus</i>) Open
Since 1998, California sea lion ( Zalophus californianus ) stranding events associated with domoic acid toxicosis have consistently increased. Outside of direct measurement of DA in bodily fluids at the time of stranding, currently there a…
View article: Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer
Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer Open
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of Q…
View article: Comment on egusphere-2023-3148
Comment on egusphere-2023-3148 Open
Abstract. Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical …
View article: Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures
Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures Open
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-la…
View article: Supplementary material to "Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures"
Supplementary material to "Results from a Multi-Laboratory Ocean Metaproteomic Intercomparison: Effects of LC-MS Acquisition and Data Analysis Procedures" Open
Informatic Intercomparison MethodologiesLab 109: The raw files were searched against the metagenomic database employing a 2 round search using PEAKS Studio X.The initial database search was performed to focus the metagenomic database for p…
View article: Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry Open
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins a…
View article: A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development Open
View article: Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin (Tursiops truncatus)
Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin (Tursiops truncatus) Open
The last decade has witnessed dramatic improvements in whole-genome sequencing capabilities coupled to drastically decreased costs, leading to an inundation of high-quality de novo genomes. For this reason, the continued development of gen…
View article: The Association of Biomolecular Resource FacilitiesProteome Informatics Research Group Study on Metaproteomics(iPRG-2020)
The Association of Biomolecular Resource FacilitiesProteome Informatics Research Group Study on Metaproteomics(iPRG-2020) Open
Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sam…
View article: 2019 Association of Biomolecular Resource FacilitiesMulti-Laboratory Data-Independent Acquisition ProteomicsStudy
2019 Association of Biomolecular Resource FacilitiesMulti-Laboratory Data-Independent Acquisition ProteomicsStudy Open
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in proteomics core facility setti…
View article: Toward an Integrated Machine Learning Model of a Proteomics Experiment
Toward an Integrated Machine Learning Model of a Proteomics Experiment Open
In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals…
View article: ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics Open
Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, du…
View article: Glycosylation and the global virome
Glycosylation and the global virome Open
The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation ‐ and harness…
View article: ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics
ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics Open
Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels…
View article: compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets
compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets Open
It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as rout…
View article: Glycosylation and the global virome
Glycosylation and the global virome Open
The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harness…
View article: Glycosylation and the global virome
Glycosylation and the global virome Open
The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harness…
View article: Glycosylation and the global virome
Glycosylation and the global virome Open
The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harness…
View article: Serum Proteomics Identifies Immune Pathways and Candidate Biomarkers of Coronavirus Infection in Wild Vampire Bats
Serum Proteomics Identifies Immune Pathways and Candidate Biomarkers of Coronavirus Infection in Wild Vampire Bats Open
The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of t…