Advanced Proteomics Techniques and Applications

A Deep Quantitative Proteome Turnover Platform for Human iPSC-derived Neurons

The paper develops a platform to measure protein turnover in human iPSC-derived neurons, revealing conserved and subtype-specific proteome dynamics.

Targeted proteomics informed by long-read RNA-sequencing reveals protein isoform expression associated with bone mineral density

This study uses genetics-guided targeted mass spectrometry to detect protein isoforms associated with bone mineral density, confirming their expression in clinical samples.

A High-Sensitivity and High-Throughput LC-MS Workflow for Low-Input and Single-Cell Proteomics

This paper develops a high-sensitivity and high-throughput LC-MS workflow for low-input and single-cell proteomics, achieving high proteome depth and throughput without specialized equipment.

PepPr: De Novo peptide sequencing with peptide priors

PepPr improves peptide sequencing by integrating peptide priors, enhancing reference and variant peptide identification while maintaining discovery flexibility.

Beyond the Axenic Culture Filtrate Secretome: BONCAT and conventional proteomics together reveal the Infection-associated secreted protein repertoire of Acinetobacter baumannii in the human lung Epithelial cell line A549

This study uses BONCAT and conventional proteomics to identify infection-associated secreted proteins of Acinetobacter baumannii in A549 cells, revealing 152 proteins not detected in axenic cultures.

MXene Protein Corona Interfaces for Molecular Profiling of Alzheimers Disease

This study uses MXene nanosheets to capture Alzheimer's disease-associated plasma protein signatures, revealing disease-specific proteomic changes and potential biomarkers.

Scanning DIA on the ZenoTOF 8600 system records a precursor dimension for every fragment at tenfold higher ion flux

The paper introduces the ZenoTOF 8600 system, which enhances proteomics by increasing ion flux and improving precursor identification and quantification in DIA mode.

TransPepMS: A Tool to Verify Peptides Absent from Reference Proteomes

TransPepMS verifies peptides not in reference proteomes by resolving ambiguities in mass-spectrometry data to distinguish genuine non-canonical peptides from false positives.

Cell-type resolved prenylomics in mouse liver enabled by a low-input proteomics workflow

This paper develops a low-input prenylomic workflow to enable cell-type-specific analysis of prenylated proteins in mouse liver tissue.

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

Asking the Data: Conversational Interrogation of LC-MS/MS Proteomics Data Sets with an LLM Agent

The paper introduces a conversational framework using an LLM agent to interrogate proteomics data sets, identifying issues in four LC-MS/MS datasets and demonstrating its feasibility in reanalyzing data.

Protein Aggregation Capture for Top-down Proteomics

This paper introduces a magnetic bead-based sample preparation method for top-down proteomics to improve sensitivity and reduce sample loss during protein aggregation capture.

Non-canonical proteoforms of the human fusiform gyrus in Alzheimers disease

The paper identifies non-canonical proteins encoded by non-coding ORFs in Alzheimer's disease, finding 67 differentially expressed proteins in the fusiform gyrus.

Joining Two Perspectives of the Proteome with the Trypsin+HTA Protease Workflow

This paper evaluates the use of HTA protease in combination with trypsin for proteomic analysis, showing increased protein and modification identifications and improved quantification.

msallsearchpy: Universal Search Engine with Enhanced Performance for High-Flow Quantitative LC-MS Proteomics

The paper introduces msallsearchpy, a search engine for high-flow quantitative LC-MS proteomics, showing improved identification and quantification performance over existing methods.

High-fidelity bispecific protease KRysin for deeper plasma proteomics and phosphoproteomics

KRysin, a bispecific protease, improves plasma and phosphoproteomics by enhancing digestion completeness and PTM coverage compared to trypsin.

Making the Impossible Possible: Uniting TMT and DIA for Scalable Low-Input-Proteomics

This paper combines TMT and DIA proteomics techniques to improve low-input proteomics, showing how to overcome co-isolation interference and enabling TMT quantification with DIA-focused software.

Sample Preparation and Homology-Driven Search Shape the First Holobiont Proteome of the Marine Sponge Viles ophiraphidites (formerly Topsentia ophiraphidites)

The paper compares sample preparation workflows and homology-driven search strategies to characterize the proteome of a marine sponge, finding S-Trap with homology layers provides the most comprehensive and consistent results.

A qualitative and quantitative framework for the characterization of protein-RNA interactions by cross-linking mass spectrometry (XL-MS)

This paper introduces a XL-MS workflow combining DDA and PRM for quantitative characterization of protein-RNA interactions, applied to TDP-43 and FOX1 complexes.

Scalable proteomics with multiDIA resolves proteoforms in neurodegenerative disease

The paper introduces multiDIA, a proteomics method that improves sequence coverage and scalability in neurodegenerative disease studies by combining multiple proteases and data-independent acquisition.

Investigating Histone Lysine Acetylation and Acetyl-methylation in Mouse Brain using Enhanced Trimethylacetic Anhydride Derivatization Protocol

This study optimizes a TMA derivatization protocol for histone PTM analysis, identifies Kacme as a novel modification, and reveals its distinct metabolic dynamics.

Subcellular spatial proteomics of the close animal relative, Capsaspora owczarzaki

This study uses subcellular spatial proteomics to map protein localization in Capsaspora owczarzaki, a close animal relative, identifying 3,106 high-confidence localizations across 13 compartments.

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Subcellular spatial proteomics of the heterotrophic nanoflagellate, Cafeteria roenbergensis

This study uses subcellular spatial proteomics to map protein localization in Cafeteria roenbergensis, identifying 2,945 proteins across 14 compartments.

FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets

The paper presents an unbiased surfaceome atlas of leukemic cell lines, identifying novel surface proteins and discordant gene expression patterns, with CD70 highlighted as a potential therapeutic target in AML.

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

mzQC: a versatile way to communicate quality information for biological mass spectrometry

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

How to design 1000-plex mass tags using the differential mass defect

This paper explores designing high-plex mass tags using differential mass defect to enable large-scale multiplexing in proteomics.

Informatics Methods to Enhance Bacterial Peptide Detection

The paper develops and benchmarks an in silico spectral library workflow to detect low-abundance bacterial peptides in human-dominated samples, finding it has complementary performance to conventional database searches.