Advanced Proteomics Techniques and Applications

Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

The paper introduces nanoSPLITS, a platform for simultaneous transcriptome and proteome profiling of single cells, and demonstrates its application in cell cycle regulation and cell type identification.

An algorithm for predicting per-cell proteomic properties

The paper develops an algorithm to estimate per-cell proteomic properties using scaling relationships, finding higher total proteins per cell than previous estimates.

A minimalist binary/digital approach to large-scale single molecule protein identification with optically labeled tRNAs and multiple carboxypeptidases and its extension to peptide sequencing

The paper proposes a minimalist binary/digital method for single molecule protein identification using optically labeled tRNAs and carboxypeptidases, achieving high identification rates for human peptides.

Leveraging the Human Panproteome to Enhance Peptide and Protein Identification in Proteomics and Metaproteomics

This paper introduces a panproteome graph to enhance peptide and protein identification in proteomics and metaproteomics by leveraging the human pangenome.

De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution

This paper introduces de novo peptide databases for Protein-SIP to analyze microbial communities with species-level resolution, showing comparable performance to genome-derived databases.

Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis.

This study compares cleavable and uncleavable biotin-alkyne labels in BONCAT analysis, finding that cleavable labels improve protein identification and quantification.

ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics

ProtPipe is a data analysis pipeline for proteomics and peptidomics that automates processing, quality control, and downstream analysis of mass spectrometry data.

Calculating and Reporting Coefficients of Variation for DIA-based Proteomics

This paper discusses the calculation and reporting of coefficients of variation in DIA-based proteomics and proposes guidelines and an R package for accurate benchmarking.

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

The paper benchmarks sequencing tools for identifying degraded proteins in ancient samples, finding optimal strategies for peptide and PTM detection.

Multimodal single cell-resolved spatial proteomics reveals pancreatic tumor heterogeneity

The paper introduces SCPro, a multimodal spatial proteomics method, to profile pancreatic tumor heterogeneity by integrating imaging, flow cytometry, and protein aggregation capture, revealing spatial proteome variations and a novel regulatory T cell subtype.

Astrocyte-specific secretome profiling reveals its correlation with neurological disorders

The paper develops a secretome profiling method for astrocytes and identifies proteins involved in disease-related toxicity and neuroprotection.

One-Pot Time-Induced Proteome Integral Solubility Alteration (OPTI-PISA) assay for automated and sensitive drug target identification

The paper introduces OPTI-PISA, a method that automates and reduces sample requirements for drug target identification, demonstrating its effectiveness in cell lysates with sub-microgram samples.

Beta-DIA: Integrating learning-based and function-based feature scores to optimize the proteome profiling of single-shot diaPASEF mass spectrometry data

Beta-DIA improves proteome profiling by combining deep learning and function-based scores for diaPASEF data, doubling protein group detection in low datasets.

Amino acid substitutomics: profiling amino acid substitutions at proteomic scale unveils biological implication and escape mechanism in cancer

This study introduces a proteomic approach to identify amino acid substitutions in cancer, revealing novel substitutions and their roles in drug resistance and immune escape.

Towards routine proteome profiling of FFPE tissue: Insights from a 1,200 case pan-cancer study

The paper profiles proteomes from 1,220 FFPE tumors across six cancers, identifies a new normalization method, and reports a comprehensive pan-cancer proteome resource.

An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS

The paper develops a robust LC-MS/MS workflow for quantifying H2AK119ub and H2BK120ub histone ubiquitination marks, improving upon existing methods for C-terminal modifications.

Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures

The paper compares Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) in TNBC samples to assess their performance and identify complementary proteomic profiles.

PhosX: data-driven kinase activity inference from phosphoproteomics experiments

PhosX infers kinase activity changes from phosphoproteomics data using substrate sequence specificity, outperforming existing methods without requiring prior kinase-substrate knowledge.

Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics

Orthrus improves metaproteomics analysis by combining de novo sequencing and database searching, outperforming existing tools in peptide output and taxonomic diversity.

Anubis: a multi-level authentication scale for ancient proteins using random forest classification

Anubis authenticates ancient proteins using deamidation patterns and random forest classification, demonstrating reliability with ancient and degraded beta-lactoglobulin.

Standard-flow targeted proteomics for quantification of enzymes in glucosinolate biosynthetic pathways

This study uses standard-flow targeted proteomics to quantify 12 enzymes in Arabidopsis thaliana's glucosinolate biosynthetic pathway, revealing correlations between transcript and protein levels under normal conditions and uncoupling under methyl-jasmonate treatment.

Parallel phosphoproteomics and metabolomics map the global metabolic tyrosine phosphoproteome

The paper identifies and validates tyrosine phosphorylation sites on metabolic enzymes using parallel phosphoproteomics and metabolomics in MCF10A cells.

DDA-BERT: leveraging transformer architecture pre-training for data-dependent acquisition mass spectrometry-based proteomics

DDA-BERT improves PSM rescoring in proteomics using a transformer-based model trained on 95 million human spectra, outperforming existing methods across species and sample types.

Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules

This paper demonstrates that adding small molecules to plasma enhances nanoparticle protein corona diversity, significantly increasing the number of detectable proteins in plasma proteome profiling.

Mass spectrometry-based proteomic exploration of diverse murine macrophage cellular models

The paper compares proteomic profiles of murine macrophage cell lines to primary and immortalised bone marrow-derived macrophages, identifying J774A.1 as the most similar to primary cells.

SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome

SysQuan uses SILAC mouse tissues as internal standards to enable affordable absolute quantitation of the human proteome, improving comparability across studies and laboratories.

Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamic interactions

This paper introduces MM-TPP, a method to map membrane protein-ligand interactions using Peptidisc and thermal proteome profiling, showing it detects specific ligand effects on ABC transporters and GPCRs better than detergent-based TPP.

PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS

The paper develops recombinant protein standards and a search engine for XL-MS, showing Scout outperforms existing tools in speed, sensitivity, and false-discovery rate control.

Hybrid Quadrupole Mass Filter Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics

The paper introduces a new MS platform with enhanced acquisition rates and real-time chromatogram alignment, enabling high multiplex targeted proteomics with improved sensitivity and throughput.

EasyAb: A High-Throughput Workflow for Antibody-Based PTM Peptide Enrichment Method Coupled to Mass Spectrometry

EasyAb is a high-throughput workflow for antibody-based PTM peptide enrichment coupled to mass spectrometry, enhancing sensitivity for large-scale PTM analysis in diverse cell systems.