Advanced Proteomics Techniques and Applications

Mass spectrometry-based top-down proteomics in nanomedicine: proteoform-specific measurement of protein corona

This study introduces a top-down proteomics method to precisely identify proteoforms in nanoparticle protein coronas, revealing biomarkers not detectable by bottom-up approaches.

Combining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification

This paper introduces DIA-SiS, a method combining DIA with spike-in SILAC to improve proteome coverage and quantification, showing better performance than label-free approaches.

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst

FragPipe-Analyst provides an R shiny web server and R package for downstream analysis and visualization of quantitative proteomics data from FragPipe.

A framework for quality control in quantitative proteomics

The paper introduces a framework for quality control in quantitative proteomics, combining internal and external QC measures with tools for data analysis and deposition.

The proteomic landscape and temporal dynamics of mammalian gastruloid development

This study uses quantitative proteomics to analyze human and mouse gastruloids at four stages, revealing protein dynamics, discordance with transcriptomes, and gene networks linked to developmental defects.

Temporal proteomic and PTMomic atlas of cerebral organoid development

This study presents a temporal atlas of protein and PTM abundance in cerebral organoids, showing significant changes during development related to neuronal differentiation and energy metabolism.

Accounting for digestion enzyme bias in Casanovo

The paper modifies the Casanovo model to account for digestion enzyme bias but finds no significant improvement in sequencing accuracy.

Native proteomics by capillary zone electrophoresis-mass spectrometry

This paper introduces a new native proteomics technique using nCZE-MS to measure proteoforms and protein complexes in complex samples, achieving high sensitivity and resolution.

Evaluating computational approaches for comparison of protein expression across cancer indications

The paper evaluates normalization strategies for creating a pan-cancer protein expression dataset from CPTAC, finding global quantile normalization most effective for cross-cohort comparisons.

Data mining antibody sequences for database searching in bottom-up proteomics

The paper extends antibody databases for mass spectrometry by mining millions of sequences from the OAS database to improve antibody peptide identification in SARS-CoV-2 plasma samples.

Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification

ProteoRift predicts peptide properties from mass spectrometry data using a deep attention-based multitask network, reducing search space and improving speed while maintaining accuracy.

Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques

This study compares SP3 and SP4 proteomics clean-up techniques, finding SP3 captures hydrophilic proteins via HILIC-like and aggregation mechanisms, while SP4 captures hydrophobic proteins via aggregation.

Proteonano: A Robust Platform for Large Cohort Deep Plasma Proteomic Studies

The paper introduces a platform for large-scale plasma proteomics studies that improves the detection of low-abundant proteins and enables biomarker discovery in neurodegenerative diseases.

An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues

This paper introduces a high-throughput proteomics workflow using Orbitrap and Astral mass analyzers, demonstrating robust sample preparation and high protein identification rates across diverse biological samples.

Back to Basics: Spectrum and Peptide Sequence are Sufficient for Top-tier Mass Spectrometry Proteomics Identification

This paper introduces a deep learning-based approach for peptide identification in mass spectrometry proteomics that outperforms existing tools by using spectra and peptide sequences directly.

Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer

The paper introduces a method using the Orbitrap Astral mass spectrometer with DIA to rapidly analyze phosphoproteomes, detecting over 80,000 phosphorylation sites in mice.

Removal of NHS-labelling by-products in Proteomic Samples

The paper develops a method to efficiently remove over-labelled peptides in proteomics samples, improving identification rates and quantitation precision.

Simplified and Rapid Workflow Enhances Throughput of De Novo Sequencing of COVID-19 Neutralizing Antibodies

This paper develops a rapid de novo sequencing workflow for COVID-19 neutralizing antibodies, achieving high accuracy in mixed antibody mixtures.

Gel-Assisted Proteome Position Integral Shift (GAPPIS) Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Novel Caspase 3 Substrates

The paper introduces GAPPIS, a method to recover molecular weight information from shotgun proteomics, identifying novel caspase 3 substrates in apoptotic cells.

A modified decision tree improves generalization across multiple brains proteomic data sets and reveals the role of ferroptosis in Alzheimer disease

The paper introduces a modified decision tree model for proteomic data analysis, improving generalization across Alzheimer's disease datasets and identifying ferroptosis-related proteins as important in dementia resistance.

PIPI-C: A combinatorial optimization framework for identifying post-translational modification crosstalks in mass spectrometry data

PIPI-C identifies PTM crosstalks in mass spectrometry data using a combinatorial optimization framework, revealing upregulated PTM patterns in cancer datasets.

Standardizing protein corona characterization in nanomedicine: a multi-center study to enhance reproducibility and data homogeneity

This study standardizes protein corona characterization across proteomics centers, improving data consistency and reproducibility through unified protocols and workflows.

Rescuing error control in crosslinking mass spectrometry

The paper identifies issues in crosslinking mass spectrometry analysis where heuristic methods can distort error estimation, leading to false protein-protein interaction discoveries and proposes ways to correct this.

mini-Complexome Profiling (mCP), an FDR-controlled workflow for global targeted detection of protein complexes

The paper introduces mCP, a streamlined workflow for detecting protein complexes with reduced fractionation, and demonstrates its application in analyzing cardiac tissue.

Sequence-to-sequence translation from mass spectra to peptides with a transformer model

Casanovo translates tandem mass spectra into peptide sequences using a transformer model, outperforming existing methods and improving analysis in immunopeptidomics and metaproteomics.

Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics

This paper discusses machine learning strategies to overcome data challenges in mass spectrometry-based proteomics, emphasizing the need for standardized datasets and larger data sizes to improve model performance.

diaPASEF Enables High-throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development

The paper evaluates diaPASEF for HCP analysis in biopharmaceutical processes, showing improved quantification and throughput compared to standard methods.

Concatemer Assisted Stoichiometry Analysis (CASA): a targeted mass spectrometry method for protein quantification

This paper introduces CASA, a targeted mass spectrometry method for protein quantification, and demonstrates its application in determining stoichiometries of kinetochore components in budding yeast.

ThunderBolt: An interactive data sharing and analysis platform for large-omics experiments

ThunderBolt provides an interactive web platform for analyzing large proteomics datasets through guided exploration, preprocessing, and statistical analysis.

Site-specific metabolic labeling reveals proteome-wide phospho-dynamics

This study introduces PulsPhos, a method to quantify site-specific phosphorylation lifetimes in living cells and applies it to pharmacological perturbations.