Brendan MacLean

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics

Carafe2 generates high-quality in silico spectral libraries for timsTOF DIA proteomics by fine-tuning deep learning models on DIA data, outperforming DDA-trained models in multiple applications.

Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer

The paper develops scalable targeted proteomics assays using the Stellar mass spectrometer for analyzing biofluids, demonstrating high sensitivity and multiplexing capabilities.

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics

Carafe generates high-quality in silico spectral libraries for DIA proteomics by training deep learning models directly on DIA data, improving fragment ion intensity prediction and peptide detection.

Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics - Beyond identification lists

This paper evaluates a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics, showing improved performance in ion detection and quantitative precision compared to the standard Orbitrap Astral MS.

Hybrid Quadrupole Mass Filter Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics

The paper introduces a new MS platform with enhanced acquisition rates and real-time chromatogram alignment, enabling high multiplex targeted proteomics with improved sensitivity and throughput.

Koina: Democratizing machine learning for proteomics research

Koina provides an open-source, accessible ML/DL prediction service for proteomics, improving integration with existing tools like FragPipe.

A Workflow for Improved Analysis of Cross-linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline

This paper introduces a workflow for improved XL-MS data analysis using PASEF, integrating MeroX and Skyline for better identification of cross-linked products.

Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity

The paper develops a multidimensional lipid library using Skyline to annotate lipidomic data and applies it to identify lipid markers for smoke inhalation injury severity.

Avant-garde: An automated data-driven DIA data curation tool.

Avant-garde improves DIA data analysis by refining signals, reducing interference, and controlling false discovery rates through a data-driven approach.

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

The paper creates a proteomic resource profiling 90 drugs in six cell lines, revealing cell-specific responses and enabling integration with transcriptional data to identify therapeutic opportunities.