Michael J. MacCoss

The paper introduces a framework for quality control in quantitative proteomics, combining internal and external QC measures with tools for data analysis and deposition.

The paper shows that a second X chromosome in aging mice improves cognition, with female gonads and sex chromosomes contributing to cognitive resilience.

This paper introduces a transformer-based model called Cascadia for de novo sequencing of data-independent acquisition mass spectrometry data, achieving state-of-the-art performance.

The paper identifies a genetic locus and protein associated with resilience to cognitive decline in AD-BXD mice and links it to human AD traits.

The paper analyzes single exosomes in CSF from Alzheimer's and Parkinson's patients and controls, finding reduced ApoE+ exosomes in Alzheimer's patients.

This study shows that enhancing skeletal muscle TFEB signaling reduces neuroinflammation and tau pathology in aging and neurodegenerative disease models.

The paper evaluates the Astral mass analyzer's performance in quantitative proteomics, showing it quantifies 5 times more peptides per unit time than existing Orbitrap mass spectrometers and detects over 5,000 plasma proteins.

This study compares FAIMS and quadrupole gas-phase fractionation in peptide identification, finding that FAIMS improves results mainly by reducing co-isolation of precursor ions and chimeric spectra.

This paper introduces a dynamic DIA mass spectrometry method that improves quantitative sensitivity by adjusting MS/MS windows during chromatographic separation.

The paper presents a high-quality quantitative proteomics dataset for Alzheimer's disease, including samples from different brain regions and clinical groups.

The paper summarizes recent developments in the Crux toolkit for analyzing bottom-up proteomics data, including speedups, new features, and tools.

The paper identifies and characterizes small ORFs and microproteins in adipose cells, showing their metabolic relevance and potential roles in obesity and inflammation.

The paper identifies proteomic features of resilience to Alzheimer's disease, finding lower soluble Aβ levels and specific protein interactions in brain regions associated with resistance to dementia.

The paper uses isotope-labeled crosslinkers to analyze protein interactions and posttranslational modifications in Diaphorina citri across life stages, revealing developmental changes in chromatin structure.

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.

The paper identifies isomerization of Asp387 in tau as a marker of reduced autophagic flux in Alzheimer's disease using mass spectrometry analysis of brain tissue.

This paper introduces a workflow to build spectral libraries from DIA mass spectrometry data, showing it can detect phosphorylated peptides and outperforms library-free methods in accuracy and sensitivity.

The paper characterizes the egg coat proteome of threespine stickleback fish and identifies evolutionary changes in ZP proteins that may contribute to reproductive isolation.

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

piNET is a web platform for analyzing and visualizing proteomics data, including PTMs, by connecting them to biological knowledge and LINCS signatures.

The paper shows that protein timecourses in yeast can be predicted from mRNA trajectories using a gene-specific model, revealing strain-specific differences in post-translational processes.

Thesaurus identifies phosphoprotein positional isomers by analyzing fragment ions from mass spectrometry data, revealing kinase-specific regulation in the PI3K/AKT pathway.

This study identifies a Stu2-mediated tension-sensing pathway that works with Aurora B to correct kinetochore attachments in vivo.

This paper summarizes current XL-MS practices, compares strategies, and proposes common protocols to establish best practice guidelines for accurate and reproducible results.

This study develops a method to quantify nuclear protein dynamics by isolating chromatin compartments and using mass spectrometry, revealing chromatin remodeling during BET protein degradation.

Specter improves DIA proteomics by directly deconvoluting spectra using linear algebra, enhancing sensitivity for similar peptides and challenging cases.

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.