Advanced Proteomics Techniques and Applications

dnoise: Fast Native Data Reduction for Bruker timsTOF

dnoise reduces Bruker timsTOF data size with minimal impact on analysis results.

ChemIntelligence Enables Antibody-Free, Ultra-Low-Input Profiling of Lysine Lactylation and Diverse Acyl-Proteomes

ChemIntelligence enables antibody-free, ultra-low-input profiling of lysine lactylation and diverse acyl-proteomes using chemical derivatization and computational methods.

Prioritizing peptides for targeted mass spectrometry experiments using deep learning

Bromo, a pairwise transformer, ranks a protein's peptide precursors by expected mass spectrometry response, beating XGBoost, PREGO and PeptideRanger on held-out yeast data, and can be fine-tuned per instrument.

Balancing spatial resolution and proteome depth in LC-MS based spatialproteomics

This study evaluates the trade-off between spatial resolution and proteome depth in spatial proteomics using SLACS, showing that few-cell sampling maintains proteomic information while increasing spatial specificity.

Recurrent non-canonical proteoforms in acute myeloid leukemia identified by integrative proteogenomics

The paper identifies recurrent non-canonical proteoforms in AML using integrative proteogenomics, revealing 5,849 unannotated proteoforms, including 1,987 with no homology to annotated proteins.

XMAn Update - A Database of Homo sapiens Mutated Peptides

XMAn Update expands a database of mutated peptides by integrating cancer-related variants from COSMIC and CGC datasets to improve variant detection in mass spectrometry analyses.

In the same cell, the proteome defines cellular state and the transcriptome marks transitions

The paper quantifies proteins and transcripts in the same cell, finding that the proteome defines stable cell states while the transcriptome reflects transitions.

Proteomic Profiling of Enriched Nuclei Provides a Nuclear Proteome Resource and Protein Interaction Landscape for Trypanosoma cruzi

The paper profiles the nuclear proteome of Trypanosoma cruzi using mass spectrometry and identifies protein interactions and modifications, providing a resource for further studies.

A tissue-resolved endothelial surface proteome atlas informs organ-selective vascular targeting

This study maps organ-specific endothelial surface proteomes in vivo to identify tissue-selective vascular targets for therapy.

Integration of proteomic data from cell lines and tumors

This paper introduces ProtInt, a deep learning framework for integrating proteomic data from cancer cell lines and tumors, showing improved performance over existing methods.

A Scalable and Robust Workflow for Cost-Effective Post-Translational Modifications Profiling by Chemical Proteomics

The paper describes a chemical proteomics workflow that reduces protein input and improves sensitivity for profiling post-translational modifications.

A generalizable normalization framework to decouple protocol and instrument effects: Application to high-sensitivity proteomics multicentric study (PME13)

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.

MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification

MARLOWE is a computational tool for taxonomic characterization of unknown forensic samples using de novo peptide identification, achieving high specificity in species-level identification.

Discovery of non-canonical proteins through modification-aware proteogenomics

This paper demonstrates that using ionbot with OpenProt improves detection of non-canonical proteins by reducing FDR and increasing reproducibility compared to TPP.

STEP-PTMs: Sequential TMT-based Enrichment and Profiling of Post-Translational Modifications

STEP-PTM enables integrated quantitative analysis of proteome, metabolome, and multiple PTM classes from single biological samples using a modular TMT-multiplexed workflow.

From variability to consensus: rescoring harmonizes peptide identification across diverse search engines and datasets

This study benchmarks rescoring methods across proteomics search engines and datasets, finding that prediction-based approaches improve identification consensus and reduce variability.

MetaPilot enables adaptive genome-aware DDA and DIA metaproteomics using microbial genome catalogues

MetaPilot improves metaproteomics analysis by using genome-aware search-space refinement, enhancing peptide identification in DDA and DIA datasets.

Spatial proteomics of the human atherosclerotic microenvironment reveals heterogeneity in intra-plaque proteomes and extracellular matrix remodeling

This paper uses spatial proteomics to reveal proteome heterogeneity and ECM remodeling in human atherosclerotic plaques across different regions.

Serum preprocessing workflows differentially shape biological readout in data-independent acquisition proteomics of systemic juvenile idiopathic arthritis

This study compares serum preprocessing workflows in proteomics to assess their impact on biological readouts in systemic juvenile idiopathic arthritis.

Reference-free protein sequencing by consensus assembly of redundant de novo peptide reads

borgonovo improves protein sequence accuracy from tandem mass spectra by consensus assembly of redundant de novo peptide reads, achieving 0.87 mean fixed-window identity on therapeutic antibodies.

Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics

The paper introduces a visualization framework for top-down proteomics data, called proteoform barcode, which displays proteoform abundance and functional information, enabling disease diagnosis.

Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks

This paper introduces a protein language model-based decoy generation method for proteomics and benchmarks it against classical decoy strategies, finding it less distinguishable by neural networks but not superior in search performance.

From Routine Pathology to Precision Oncology: Automated FFPE Tissue Processing for Large-Scale Molecular Studies

The paper develops an automated FFPE deparaffinization workflow to improve protein yield and reproducibility in melanoma studies.

Benchmarking Spectral Library Prediction Platforms for Neuropeptidomics Applications

This study benchmarks four spectral prediction platforms for neuropeptidomics, finding no single model captures neuropeptide fragmentation well and highlighting the importance of neutral loss fragments and hybrid libraries.

Top-down Sequencing of Intact Proteoforms using the timsOmni mass spectrometer: Accurate Determination of Co-occurring Histone Modifications

This study uses multimodal mass spectrometry to accurately map co-occurring histone modifications on intact proteins, enabling residue-level assignment of modifications and positional isomers.

A detergent-free workflow for native membrane proteomics using Peptergents

This paper introduces Peptergents, a detergent-free method for native membrane proteomics that preserves protein structure and function, enabling better analysis of membrane proteins and their interactions.

GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

GenomeProt integrates genomics, transcriptomics, and proteomics to characterise proteoforms, discovering novel proteins and variant-containing peptides in human brain and melanoma samples.

Mapping the Architecture of Protein Complexes in Arabidopsis Using Cross-Linking Mass Spectrometry

This study maps protein-protein interactions in Arabidopsis using cross-linking mass spectrometry, identifying thousands of interactions across subcellular compartments and structural complexes.

MSstatsResponse: Semi-parametric statistical model enhances detection of drug-protein interactions in chemoproteomics experiments

MSstatsResponse improves detection of drug-protein interactions in chemoproteomics by using a semi-parametric statistical model that avoids fixed curve shapes, enhancing accuracy and robustness in low-replicate and low-dose settings.

Discovery and Targeting of a Cryptic Human Proteome

The paper introduces RyboCypher, a platform that maps the dark transcriptome to unannotated peptides, identifying cryptic proteins in cancer cell lines, tumors, and healthy tissues.