M. Mann

Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

This study uses Deep Visual Proteomics to analyze proteomic profiles in composite Hodgkin and small lymphocytic lymphomas, identifying subtype-specific treatment strategies.

A novel hybrid high speed mass spectrometer allows rapid translation from biomarker candidates to targeted clinical tests using 15N labeled proteins

The paper introduces a novel hybrid mass spectrometer, Stellar MS, enabling rapid and sensitive clinical biomarker validation using 15N labeled proteins.

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

The paper develops a method combining multiplexed imaging and proteomics to analyze tumor microenvironments, identifying immune cell interactions and adaptations in colorectal and tonsil cancers.

Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation

The paper uses Deep Visual Proteomics to show that human colon organoids switch to an in vivo-like phenotype after xenotransplantation.

Systematic mapping of MCU-mediated mitochondrial calcium signaling networks

This study maps the MCU-mediated mitochondrial calcium signaling network using proteomics, identifying 89 new interactors and their roles in disease-related pathways.

Grove-level analysis of titer and prevalence of Candidatus Liberibacter asiaticus and Wolbachia in Diaphorina citri, vector of citrus Huanglongbing

The paper measures CLas and Wolbachia titers in D. citri from Florida groves with different HLB management strategies, finding that grove site significantly affects CLas titer and wDi titer correlates with non-infected insects.

Inhibition of mammalian mtDNA transcription paradoxically activates liver fatty acid oxidation to reverse diet-induced hepatosteatosis and obesity

The paper shows that inhibiting mitochondrial DNA transcription in mice increases fatty acid oxidation, reducing obesity and liver fat while decreasing oxidative phosphorylation capacity.

The potential of plasma HLA peptides beyond neoepitopes

The paper develops a sensitive method to analyze HLA peptides in plasma, revealing stable and tissue-representative immunopeptidomes with potential for biomarker discovery.

SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection

This study identifies a novel interaction between SARS-CoV-2 NSP3 and FMRPs, showing that this interaction is critical for viral replication and disease progression.

In depth profiling of the cancer proteome from the flowthrough of standard RNA-preparation kits for precision oncology

The paper demonstrates that high-quality proteomics data can be obtained from Qiagen AllPrep flowthroughs, enabling efficient multi-omics analysis from the same biopsy.

AlphaPeptStats: an open-source Python package for automated, scalable and industrial-strength statistical analysis of mass spectrometry-based proteomics

AlphaPeptStats provides a Python package for scalable statistical analysis of proteomics data, offering tools for normalization, visualization, and automated statistical tests.

A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics

This paper introduces a workflow for using membrane glass slides in histology and spatial proteomics, improving compatibility with automated staining and preserving antigen retrieval.

Activity-based profiling of cullin-RING ligase networks by conformation-specific probes

The paper develops conformation-specific probes to profile activated cullin-RING ligase networks, revealing differential regulation across cell types and activation pathways.

Consistency across multi-omics layers in a drug-perturbed gut microbial community

The paper examines consistency and complementarity across five omics layers in a drug-perturbed gut microbial community, finding high agreement in species abundance and functional insights from different data types.

A clickable photosystem I, ferredoxin, and ferredoxin NADP+ reductase fusion system for light-driven NADPH regeneration

The paper develops a clickable fusion system for in vitro NADPH regeneration using photosystem I, ferredoxin, and ferredoxin NADP+ reductase components from cyanobacteria.

Fibroblasts-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis

This study identifies fibroblast-derived extracellular vesicles containing SFRP1 that contribute to pulmonary fibrosis and suggests SFRP1 as a therapeutic target.

Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition

This paper introduces synchro-PASEF, a method that improves fragment ion extraction and interference removal in DIA proteomics by synchronizing ion mobility and mass dimensions.

Proteogenomic analysis reveals RNA as an important source for tumor-agnostic neoantigen identification correlating with T-cell infiltration

This study identifies RNA as a significant source of tumor-agnostic neoantigens, which correlate with T-cell infiltration in multiple cancer types.

Comprehensive chromatin proteomics resolves functional phases of pluripotency

The paper develops a proteomic method to analyze chromatome dynamics during pluripotency phases, revealing regulatory complex binding and rearrangements.

Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF

This paper introduces an optimized dia-PASEF method with variable isolation windows to enhance proteome and phosphoproteome coverage in mass spectrometry.

Mitochondrial phosphoproteomes are functionally specialized across tissues

The paper quantitatively profiles mitochondrial proteomes and phosphoproteomes across multiple tissues in mice, revealing tissue-specific kinase and phosphatase repertoires and functional phosphorylation events.

Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry

This study uses top-down mass spectrometry to analyze O-glycoform changes in the Omicron S-RBD variant compared to wild-type and Delta, revealing novel glycosites and structural heterogeneity.

Direct DNA sequencing of "Candidatus Liberibacter asiaticus" from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

This paper develops a DNA sequencing protocol to directly sequence CLas and the microbiome from D. citri, revealing genetic variants and implications for citrus greening disease management.

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

The paper develops an ingestible device to collect intestinal samples and identifies regional differences in microbiota and bile acids compared to stool.

Differential UBE2H-CTLH E2-E3 ubiquitylation modules regulate erythroid maturation

The paper identifies UBE2H-CTLH ubiquitylation modules that regulate stages of human erythropoiesis, showing their role in controlling maturation and heme synthesis.

Proteomics of spatially identified tissues in whole organs

This paper introduces DISCO-MS, a method for spatial proteomics of whole organs, and shows it provides proteomics data comparable to fresh tissues in rodent and human samples.

A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters

The paper shows that the GID E3 ligase system regulates plasma membrane transporters through a stress-specific substrate receptor, Gid10, and ubiquitinates Art2.

Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes and normal tissues

The paper uses proteomics to compare metabolic pathways across tissues in prediabetes, type 2 diabetes, and normal controls, identifying tissue-specific metabolic dysregulation.

Scaling of cellular proteome with ploidy

The paper investigates how gene expression scales with ploidy in budding yeast and identifies a conserved mTORC1-S6K-Tup1 pathway that regulates proteome remodeling.

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

The paper identifies coronavirus-host protein interaction motifs, revealing SARS-CoV-2 specific mechanisms and a peptide-based inhibitor that blocks infection.