S. A. Carr

Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

This study presents an automated single-cell proteomics workflow that identifies over 4,000 proteins per cell and detects key regulatory proteins in LPS-perturbed THP-1 cells.

Structural basis for recognition of unfolded proteins by the ER stress sensor ERN1/IRE1α

This study identifies a 7-residue motif in unfolded proteins recognized by IRE1LD, revealing how IRE1 detects misfolded proteins to trigger the UPR.

The HLA-II immunopeptidome of SARS-CoV-2

The paper identifies SARS-CoV-2 peptides presented by HLA-II complexes, showing their association with CD4+ T cell epitopes and distinct targeting of viral proteins compared to HLA-I.

Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry

This paper develops a high-throughput, sensitive MS-based immunopeptidomics workflow to identify HLA-I and HLA-II peptides from tumor samples, achieving improved coverage with reduced sample requirements.

Dynamic mapping of proteome trafficking within and between living cells by TransitID

TransitID maps proteome trafficking between cellular compartments and between cells with nanometer resolution, revealing new roles for stress granules and intercellular signaling.

ESCRT-dependent STING degradation curtails steady-state and cGAMP-induced signaling

The paper identifies an ESCRT complex that degrades STING to suppress its signaling, showing its role in maintaining immune homeostasis.

Huntingtin turnover: Modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550

The paper identifies phospho-sites in huntingtin, showing PKA phosphorylation of Ser2550 in the C-HEAT domain accelerates its degradation.

A genetic model for in vivo proximity labeling of the mammalian secretome

This paper introduces a genetic mouse model for in vivo proximity labeling of the secretome, revealing organ-specific secretory profiles and serum trafficking.

OGT controls mammalian cell viability by regulating the proteasome/mTOR/mitochondrial axis

This study identifies OGT's role in maintaining cell viability by regulating the proteasome/mTOR/mitochondrial axis through amino acid homeostasis and mitochondrial fitness.

MONTE enables serial immunopeptidome, ubiquitylome, proteome, phosphoproteome, acetylome analyses of sample-limited tissues

MONTE enables serial multi-omic analysis of immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue samples, preserving precious human material and identifying immunotherapeutic targets.

Novel antibodies for the simple and efficient enrichment of native O-GlcNAc modified peptides

The paper introduces new anti-O-GlcNAc antibodies for efficient enrichment of native O-GlcNAc modified peptides, identifying over 1,300 unique peptides with reduced sample and time requirements.

Optimized liquid and gas phase fractionation increase HLA-peptidome coverage for primary cell and tissue samples

The paper improves HLA-peptidome coverage using optimized liquid and gas phase fractionation methods, enabling detection of more peptides from limited clinical tissue samples.

Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment

The paper automates the UbiFast method to enable high-throughput, multiplexed ubiquitylation profiling, identifying ~20,000 sites from 500 g input in ~2 hours with improved reproducibility and scalability.

BCOR and BCORL1 mutations disrupt PRC1.1 repressive function in leukemia by unlinking the RING-PCGF1 enzymatic core from target genes

This study shows BCOR and BCORL1 mutations disrupt PRC1.1 function in leukemia by separating its enzymatic core from chromatin targets, leading to treatment resistance.

Proximity-labeling reveals novel host and parasite proteins at the Toxoplasma parasitophorous vacuole membrane

Highly multiplexed quantitative phosphosite assay for biology and preclinical studies

The paper introduces SigPath, a mass spectrometry assay that quantifies 284 phosphosites across 200 phosphoproteins, revealing new insights into phospho-signaling in cancer models and human tumors.

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs

The paper identifies HLA-I peptides from SARS-CoV-2 in infected cells, revealing epitopes from both canonical and out-of-frame ORFs, which could inform vaccine development.

A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells

This study maps direct RNA-protein interactions of SARS-CoV-2 RNA in infected human cells using RAP-MS, identifying host factors, regulators, and potential drug targets involved in viral replication and host defense.

Dual Functions of SPOP and ERG Dictate Androgen Therapy Responses in Prostate Cancer

This study shows that SPOP and ERG mutations in prostate cancer have opposing effects on androgen receptor signaling and therapy response.

Split-TurboID enables contact-dependent proximity labeling in cells

Split-TurboID enables proximity labeling at organelle contact sites by splitting the TurboID enzyme and reconstituting it at these sites, identifying over 100 endogenous proteins.

Proteomics of protein trafficking by in vivo tissue-specific labeling

The paper develops an in vivo platform to study secreted protein trafficking between organs, identifies interorgan communication factors, and finds conserved adipokines affecting muscle activity.

CBL mutations promote activation of PI3K/AKT signaling via LYN kinase

The paper investigates how CBL mutations drive oncogenesis by enhancing LYN kinase activity and PI3K/AKT signaling, suggesting LYN inhibition as a therapeutic strategy.

Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling

This study compares proteomic and transcriptomic profiles of KRAS and RIT1 mutant lung cells to identify shared and divergent functions in oncogenic signaling.

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

The paper identifies thousands of novel unannotated proteins in cancer that contribute to the MHC I immunopeptidome, expanding potential targets for immunotherapy.

A conserved translation factor is required for optimal synthesis of a membrane protein family in mycobacteria

This study identifies LepA as a conserved GTPase that enhances the synthesis of mycobacterial porins, affecting drug tolerance and membrane permeability.

Microscaled Proteogenomic Methods for Precision Oncology

This study develops microscaled proteogenomic methods for cancer analysis, showing treatment response and resistance mechanisms in ERBB2-positive breast cancers.

Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS

This study demonstrates that dual protease type XIII/pepsin digestion improves HX-MS analysis of histone tails by providing better resolution and peptide overlap.

UbiFast, a rapid and deep-scale ubiquitylation profiling approach for biology and translational research

UbiFast enables rapid, high-throughput ubiquitylation profiling of up to 10,000 sites from small tissue samples, with applications in cancer research.

Tetracyclines Modify Translation By Targeting Key Human rRNA Substructures.

This study identifies tetracyclines as targeting human rRNA substructures, modifying translation and activating the ISR, which correlates with their anti-proliferative effects in cancer cells.

Directed evolution of TurboID for efficient proximity labeling in living cells and organisms

The paper develops TurboID and miniTurbo, biotin ligase mutants with enhanced catalytic efficiency for proximity labeling in cells and organisms, significantly reducing labeling time and toxicity.