M. J. MacCoss

A framework for quality control in quantitative proteomics

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 kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression.

This study shows that Kif9 regulates centriolar satellite positioning and mitotic progression by affecting centrosome maturation and proteostasis.

Comparing peptide identifications by FAIMS versus quadrupole gas-phase fractionation

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.

Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome

Mag-Net enriches membrane-bound particles from plasma to identify disease-specific proteins, discovering 204 proteins differentiating Alzheimer's disease dementia from controls.

Evaluating the performance of the Astral mass analyzer for quantitative proteomics using data independent acquisition

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.

MBNL1 regulates programmed postnatal switching between regenerative and differentiated cardiac states.

This study identifies MBNL1 as a regulator of cardiac cell state transitions, showing it controls RNA stability to switch between regenerative and differentiated states.

Elamipretide Improves ADP Sensitivity in Aged Mitochondria by Increasing Uptake through the Adenine Nucleotide Translocator (ANT)

This paper shows that Elamipretide improves ADP sensitivity in aged mitochondria by enhancing ADP uptake through the ANT, leading to improved muscle and heart function.

De novo design of high-affinity protein binders to bioactive helical peptides

This paper designs high-affinity protein binders for bioactive helical peptides using deep learning and generative models, achieving picomolar affinity without experimental optimization.

Elamipretide (SS-31) Treatment Attenuates Age-Associated Post-Translational Modifications of Heart Proteins

This study investigates how elamipretide affects age-related post-translational modifications in mouse heart proteins, finding that it reverses oxidative changes but not phosphorylation changes.

Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry

This study identifies novel SARS-CoV-2 epitopes using mass spectrometry and validates their immunogenicity by T cell recognition.

Discovery and visualization of uncharacterized drug-protein adducts using mass spectrometry.

The paper introduces Magnum, an algorithm for identifying drug-protein adducts, and Limelight, a tool for analyzing and visualizing adduct data, validated with CYP3A4 examples.

Identification of Actin Filament Interactors in Giardia lamblia

This study identifies 46 putative actin filament interactors in Giardia lamblia, including proteins localized to the ventral disc, suggesting a role for GlActin in host attachment.

Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring

This study compares unit resolution and high-resolution mass spectrometry for parallel reaction monitoring, finding similar precision but better sensitivity with unit resolution for most peptides.

Stage-specific, morphological and molecular markers of encystation in Giardia lamblia

This paper introduces a staging system for Giardia encystation based on ESV morphology and molecular markers, validated through GlRac and Rab GTPase analysis.

Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics?

The paper questions the assumption that all peptides from a protein coding gene represent the same protein quantity in bottom-up proteomics, highlighting the need for better methods to account for proteomic complexity.

The innate immunity protein C1QBP functions as a negative regulator of circulative transmission of Potato leafroll virus by aphids

This study identifies C1QBP as a negative regulator of Potato leafroll virus transmission by aphids using AP-MS and functional assays.

CM1-driven assembly and activation of Yeast γ-Tubulin Small Complex underlies microtubule nucleation

This study elucidates the role of the CM1 motif in Spc110p in facilitating γ-Tubulin Small Complex (γTuSC) assembly and γ-Tubulin Ring Complex (γTuRC) formation in yeast.

Late-life restoration of mitochondrial function reverses cardiac dysfunction in old mice

This study shows that treating old mice with SS-31 improves cardiac diastolic function by reducing mitochondrial oxidative stress and restoring redox balance.

Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics

The paper demonstrates how to assess quantitative peptide measurements in proteomics using matrix-matched calibration curves and shows that more detected peptides do not guarantee more quantitatively measurable peptides.

Isolation and characterization of extracellular vesicles from Caenorhabditis elegans for multi-omic analysis.

This paper isolates and characterizes extracellular vesicles from C. elegans, showing they share key properties with mammalian EVs and enabling multi-omic analysis.

Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries

The paper introduces a workflow and software tool, EncyclopeDIA, to improve peptide quantification in DIA mass spectrometry by using chromatogram libraries calibrated to specific instruments.

Novel phosphorylation states of the yeast spindle pole body

The paper reports a phosphoproteomic analysis of yeast spindle pole bodies (SPBs) under two cell cycle conditions, identifying novel phosphorylation sites on γ-TuSC that regulate microtubule nucleation and spindle length.

The human Ska complex and Ndc80 complex interact to form a load-bearing assembly that strengthens kinetochore-microtubule attachments

This study shows the Ska complex directly strengthens kinetochore-microtubule attachments by forming a load-bearing connection with the Ndc80 complex and microtubule tips.

Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana

This study identifies time-specific interactors of the plant protein GIGANTEA using proteomics, revealing a new flowering regulator and non-rhythmic partners involved in proteostasis and metabolism.