Seth Just

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics

Lee S. Cantrell, Seth Just, Alexey Stukalov, Omid C. Farokhzad et autres

Modern DIA proteomics increasingly emphasizes throughput and depth for large-cohort studies, but methods are often optimized using proxy metrics that can mask losses in quantifiable signal and statistical power. Here, we evaluate how data points per peak and other chromatographic features jointly …

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Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

Ting Huang, Jian Wang, Alexey Stukalov, Simion Kreimer et autres

The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dynamic range of protein abundances. Here, we evaluate its quantitative performance and suitability for large-scale studies. …

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Cloud-Enabled Scalable Analysis of Large Proteomics Cohorts

Harendra Guturu, Andrew Nichols, Lee S. Cantrell, Seth Just et autres

Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies enable large-scale cohort proteomic and proteogenomic analyses. As such, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in search engines that rely …

Cloud-enabled Scalable Analysis of Large Proteomics Cohorts

Harendra Guturu, Andrew Nichols, Lee S. Cantrell, Seth Just et autres

Abstract Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies are enabling large-scale cohort proteomic and proteogenomic analyses. As such studies scale, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in …

Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics

Ting Huang, Jian Wang, Alexey Stukalov, Margaret K. R. Donovan et autres

Background: The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic …

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nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows

Carolyn Allen, Rico Meinl, Sebastian Juan Paez, Brian C. Searle et autres

Data-independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the …

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Noble-Lab/crema

Donavan See, Andy Lin, Will Fondrie, Seth Just et autres

Confidence Estimation for Mass Spectrometry Proteomics. Crema is an open-source Python tool that estimates the false discovery rate (FDR) of a set of peptide-spectrum matches that result from proteomics data analysis. Crema implements standard FDR estimation methods that are widely used within …

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nf-encyclopedia: A cloud-ready pipeline for chromatogram library data-independent acquisition proteomics workflows

Carolyn Allen, Rico Meinl, Brian C. Searle, Seth Just et autres

Abstract Data independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to …

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Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

Lindsay K. Pino, Seth Just, Michael J. MacCoss, Brian C. Searle

Data independent acquisition (DIA) is an attractive alternative to standard shotgun proteomics methods for quantitative experiments. However, most DIA methods require collecting exhaustive, sample-specific spectrum libraries with data dependent acquisition (DDA) to detect and quantify peptides. In addition to working with non-human …

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Information flow analysis for javascript

Seth Just, Alan Cleary, Brandon Shirley, Christian Hammer

Modern Web 2.0 pages combine scripts from several sources into a single client-side JavaScript program with almost no isolation. In order to prevent attacks from an untrusted third-party script or cross-site scripting, tracking provenance of data is imperative. However, no browser offers …

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