Advanced Proteomics Techniques and Applications

ProtPipe2 provides a unified framework for downstream proteomics analysis across mass spectrometry, Olink, and SomaScan platforms, enabling consistent workflows and reusable analyses.

The paper investigates the proteome's role in Mycoplasma gallisepticum under stress, finding it functions as an active regulatory system through physicochemical properties and dynamic complex rearrangements.

The paper develops nanoMAPS, a droplet-based magnetic affinity purification system for surfaceome profiling of 100-500 cells, improving recovery and reducing non-specific absorption.

LRP2 is a proteogenomics pipeline that integrates long-read RNA sequencing and mass spectrometry to detect novel protein isoforms and improve their translation inference.

The paper introduces DASH-PISA, a method for automated thermal proteome profiling that enables high-throughput compound screening by improving efficiency and reducing costs.

KSTAR v1.2 improves speed and accessibility for kinase activity inference from phosphoproteomic data without compromising accuracy.

PAQu estimates protein isoform abundances using multiomic data, outperforming existing methods and revealing increased C4A isoform levels in schizophrenia.

The paper presents APT, a resource that evaluates proteomics platforms and provides decision tools to select or combine them based on study requirements.

The paper examines how changes to UniProtKB and taxonomic restrictions affect metaproteomics analysis, finding reduced peptide mapping coverage but stable dominant taxonomic profiles.

ProteoformTracker models MS signals and evaluates proteoform detectability in top-down and middle-down proteomics for experimental planning.

The paper develops a computational method to deconvolve cell cycle-dependent protein dynamics from bulk proteomics data in budding yeast and identifies 563 proteins with such dynamics.

The paper maps the spatial and structural proteome architecture of HEK293 cells using subcellular fractionation and cross-linking mass spectrometry, identifying residue-level protein interactions and expanding the human cell interactome.

This study identifies proteome-level amino acid substitutions in Alzheimer's disease using proteomic datasets and a specialized pipeline, revealing novel substitutions not detectable through genomic or transcriptomic methods.

The paper uses single-cell proteomics and transcriptomics to reveal cell-type-specific functional coordination in PBMCs, showing protein covariation that reflects protein-protein interactions and pathway rewiring.

AlphaPeptTools provides a scverse-native Python package for analyzing MS-based proteomics data, enabling scalable analysis and integration with other modalities.

CasanovoGUI provides a user-friendly desktop interface for Casanovo, a deep learning model for de novo peptide sequencing, simplifying setup and result interpretation.

SpectroVQ improves proteomics data compression and peptide identification by using a noise-aware vector-quantized autoencoder to retain useful signals and enhance library searches.

Pioneer and Altimeter provide fast, accurate analysis of DIA proteomics data, improving peptide coverage and speed compared to existing tools.

The paper benchmarks nDIA and related proteomics methods, showing nDIA with DIA-NN and Tesorai Search provides high coverage and reliable results in proteomic analysis.

This study systematically evaluates PISA assay parameters and applies them to discover a new peptide-protein interaction involving angiotensin II.

This paper introduces a platform called ProteoParcel that combines whole-cell imaging with single-cell mass spectrometry proteomics for breast cancer cells.

This paper introduces InstaNovo-FM, a self-supervised foundation model for proteomics that learns from tandem mass spectra to enable transferable applications across datasets and instruments.

The paper uses integrated mass spectrometry to show AMPK phosphorylation occurs through hierarchical proteoform cascades with specific kinetic priorities and regulatory control.

pyXLMS simplifies crosslinking mass spectrometry analysis by integrating search engine results with downstream tools, enabling non-experts to perform comprehensive analyses.

Hex-MASP enables high-resolution whole-tissue spatial proteomics mapping in mouse brains, revealing regional protein heterogeneity and antibody distribution.

The paper uses crosslinking mass spectrometry to map protein interactions in Toxoplasma gondii, identifying novel components of essential complexes and revealing structural diversity in mitochondrial machinery.

The paper demonstrates that background proteome correction improves the accuracy of identifying dynamic protein-protein interactions by reducing false positives and negatives in AP-MS experiments.

AutoBlot enables deterministic single-cell western blotting, revealing proteomic diversity in rare cell populations with high occupancy and resolution.

The paper introduces MiraProt, an R Shiny platform for proteomics analysis, and applies it to study protein changes in Mueller cells from horses with equine recurrent uveitis.

The paper integrates mRNA and protein isoform data in human RPE-1 cells to reveal widespread translation of alternative transcripts and proteolytic processing as a major source of proteome complexity.