Advanced Proteomics Techniques and Applications

SPIN: Inkjet-Driven Nanowell Workflow for Scalable and Sensitive Single-Cell Proteomics

The paper introduces a single-cell proteomics workflow using an inkjet printer and nanowell chip to improve protein recovery and throughput.

Shining a light on the dark Nt-acetylome by integrating omics data

The paper integrates COFRADIC and sel-TRAP data to refine Nat substrate specificities and uncover cryptic Nt-acetylome substrates from alternative translation initiation.

Classification with Missing Data - A NIFty Pipeline for Single-Cell Proteomics

NIFty is a classification pipeline for single-cell proteomics that handles missing data, avoids circular analysis, and mitigates batch effects without correction.

Single Cell Proteomics Reveals Novel Cell Phenotypes in Marfan Mouse Aneurysm

This paper uses single-cell proteomics to identify novel cell phenotypes in Marfan mouse aorta, revealing sex differences and angiotensin signaling roles in aneurysm formation.

Fine-Tuning of Label-Free Single-Cell Proteomics Workflows

The paper optimizes label-free single-cell proteomics workflows to achieve robust quantification of up to 5,000 proteins per Hela cell at 55 samples-per-day throughput.

The Peptonizer2000: bringing confidence to metaproteomics

The paper introduces Peptonizer2000, a tool that improves taxonomic identification in metaproteomics by combining peptide scores and taxon links with statistical models, showing higher specificity and confidence.

Generalizable direct protein sequencing with InstaNexus

This paper introduces a workflow for direct protein sequencing using AI-driven methods, validated across diverse proteins to improve accuracy and reduce ambiguity in therapeutic and scientific applications.

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform

The paper introduces TMT-Integrator, a tool for analyzing isobaric proteomic data, showing improved performance in protein and phosphorylation site quantification compared to existing tools.

High resolution, proteome-wide mapping of subcellular protein localization in plants

The paper presents an experimental strategy to map subcellular protein localization in plants using mass spectrometry, annotating thousands of proteins across multiple species and demonstrating conservation and dynamic changes.

Scalable mass-spectrometry-based molecular phylogeny with TreeMS2

TreeMS2 constructs molecular phylogenies from raw MS/MS data, revealing relationships based on molecular phenotype and identifying deviations from genetic-based trees.

Is Protein Quantification and Physical Normalization Always Necessary in Proteomics?

This study investigates whether protein quantification and physical normalization are necessary in proteomics by comparing normalized and unnormalized sample inputs, showing that computational normalization can reduce variability in some cases.

High Resolution Multi-Pass Astral Analyzer Quantification Enables Highly Multiplexed 35-Plex Tandem Mass Tag Proteomics

This paper introduces a high-resolution multi-pass Astral analyzer mode for TMT proteomics, enabling 35-plex quantification with improved depth and precision.

Single-cell nanodroplet processing proteomics pipeline for analysis of human-derived microglia

This paper introduces a single-cell proteomics pipeline for analyzing human microglia, identifying 1039 proteins per cell and revealing mitochondrial protein variation across subtypes.

Pho-Tip: one-pot dephosphorylation for rapid and sensitive analysis of DIA phosphoproteomics data

Pho-Tip is a one-pot dephosphorylation method that improves the detection of low-abundant phosphorylated peptides in DIA phosphoproteomics data.

Direct empirical in-house assessment of peptide proteotypicity for targeted proteomics

The paper assesses peptide proteotypicity in-house for targeted proteomics by synthesizing and verifying peptides from three plasma proteins.

High-throughput chemical proteomics workflow for profiling protein citrullination dynamics

The paper develops a chemical proteomics workflow to profile protein citrullination dynamics, achieving high sensitivity and throughput in detecting citrullinated peptides across biological systems.

Seamless workflow of hydroxy acid-modified metal oxide chromatography for rapid and sensitive phosphoproteomics sample preparation

This paper introduces Rapid HAMMOC, a phosphoproteomics workflow that improves sensitivity and reduces sample loss, identifying more phosphosites from low-input samples.

Single cell spatial proteomics maps human liver zonation patterns and their vulnerability to fibrosis

This study uses single-cell spatial proteomics to map human liver zonation patterns and shows their disruption in fibrosis.

High-Sensitive Spatial Proteomics for Pancreatic Cancer Progression Analysis

This study develops a high-sensitivity spatial proteomics method, SP-Max, to analyze protein expression changes in pancreatic tissues from normal to cancerous states.

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

Democratised single cell proteomics uncovers tumor associated macrophage signature in CYLD cutaneous syndrome skin tumors

The paper introduces a cost-effective single-cell proteomics method to analyze skin tumors in CYLD cutaneous syndrome, identifying a novel tumor-associated macrophage signature.

Advancing DIA-based Limited Proteolysis Workflows: introducing DIA-LiPA

The paper evaluates library-free DIA workflows for LiP-MS and introduces DIA-LiPA, a pipeline that improves structural interpretation of limited proteolysis data.

The yeast peroxisomal proteome at absolute quantitative scale

This study quantifies the yeast peroxisomal proteome under different metabolic conditions, revealing significant changes in protein abundance related to metabolic functions.

xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data

xTracer identifies peptides in PAMAF data by integrating chromatogram and mobiligram correlations, improving identification accuracy over single-domain methods.

Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome

This study uses PAMAF mode HRIM-MS to quantify succinylation sites in mouse kidney, showing Sirt5 regulates succinylation of mitochondrial proteins involved in metabolism.

Evaluation and application of chemical decrosslinking in the context of histopathological spatial proteomics

This study evaluates chemical decrosslinking to improve proteome coverage in FFPE tissues, finding that 3,4-diaminobenzoic acid enhances precursor identifications in pancreatic samples.

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

AbNovoBench: a resource and benchmarking platform for monoclonal antibody de novo sequencing

AbNovoBench benchmarks de novo sequencing algorithms for monoclonal antibodies using a large dataset and provides an online platform for antibody sequencing workflows.

Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site

The paper introduces AFDIP, a chemical proteomics method that identifies drug target binding sites with high structural resolution using digestion rate analysis and MD simulations.

PTMOverlay: A Proteomic Tool to Visualize Post-Translational Modifications Across Evolution

PTMOverlay visualizes post-translational modifications across species by aligning PTM sites to protein sequences, revealing conserved modifications in bacterial central carbon metabolism.