Advanced Proteomics Techniques and Applications

DIA-MS based plasma peptidomic workflow for profiling organ-derived peptides

This paper develops a DIA-MS workflow to identify organ-derived peptides in plasma, finding over 2,000 organ-specific peptides including 19 bioactive ones.

Quantifying the ~75-95% of Peptides in DIA-MS Datasets that were not Previously Quantified

The paper introduces an algorithm called GoldenHaystack that improves peptide quantification in DIA-MS data by quantifying previously unquantified peptides and achieving faster runtime.

Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day

This paper develops a high-throughput single-cell proteomic method for PBMCs, achieving 660 cells per day with 750 protein identifications per cell and identifying low-frequency cell types.

Enhancing Proteoform Sequence Coverage Using Top-Down Mass Spectrometry with In-Source Fragmentation and Middle-Down Mass Spectrometry

This study evaluates top-down and middle-down mass spectrometry approaches to enhance proteoform sequence coverage using in-source fragmentation and partial digestion, achieving over 90% coverage for three proteins.

Improved open modification searching via unified spectral search with predicted libraries and enhanced vector representations in ANN-SoLo

The paper enhances ANN-SoLo for open modification searching by integrating predicted spectral libraries and improved vector representations, improving peptide identification in complex proteomics workflows.

Decades of dreams coming true: capillary zone electrophoresis-mass spectrometry for reproducible multi-level proteomics

The paper demonstrates that capillary zone electrophoresis-mass spectrometry (CZE-MS) can reproducibly measure peptides, proteoforms, and complexoforms across multiple biological samples.

Native Mass Spectrometry-Based Proteomics Reveals the Mechanism of Hemophore Release by Pathogenic Corynebacterium diphtheriae

This study introduces ProteoMIX, a native top-down proteomics method to identify hemophores in C. diphtheriae, revealing protease-mediated release of soluble heme-binding proteoforms.

Single Cell Proteomics in the Developing Human Brain

This study develops a single-cell proteomics workflow to analyze the developing human brain, revealing transcriptome-proteome discordance and identifying molecular vulnerabilities in neurodevelopmental disorders.

Subcellular Mass Spectrometry Reveals Proteome Remodeling in an Asymmetrically Dividing (Frog) Embryonic Stem Cell

The paper develops a subcellular proteomics method to quantify proteins in asymmetrically dividing frog embryonic stem cells and identifies molecular changes in their descendants.

High Recovery Stop-and-Go Extraction Tips Using Polytetrafluoroethylene Disks Embedded with Poly(styrene-divinylbenzene) Particles for Proteomics

This paper evaluates two SDB-containing PTFE disks for proteomics, finding one provides better peptide recovery, especially for low-input samples.

The E. coli PeptideAtlas Build: Characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

The paper presents the E. coli PeptideAtlas build, a comprehensive pan-proteome resource covering 4,755 proteins and over 10,000 PTM sites from 40 datasets.

Deeper neuronal and glial proteomic insights using an optimized pipeline for proximity labeling proteomics

The paper optimizes a proximity labeling proteomics pipeline to enhance proteome coverage in neuronal and glial cells, revealing deeper insights into their biological functions and disease relevance.

MoDPA: Inferring Modification-dependent Protein Associations from Uniformly Reprocessed Mass Spectrometry

MoDPA infers modification-dependent protein associations from reprocessed mass spectrometry data, identifying clusters of modified proteins involved in specific biological pathways.

Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics

The paper introduces a new data structure and fragment weighting method to improve the speed and accuracy of protein quantification in mass spectrometry-based proteomics.

High-quality proteins and RNAs extracted from exact same samples for proteomics and RNA-Seq analyses

The paper describes a method to simultaneously extract high-quality RNA and proteins from the same mosquito samples, enabling both RNA-Seq and LC-MS proteomic analyses.

Highly Repeatable Tissue Proteomics for Kidney Transplant Pathology: Technical and Biological Validation of Protein Analysis using LC-MS/MS

This paper validates a mass spectrometry-based proteomics workflow for kidney transplant biopsies, showing high repeatability and clinical relevance of protein analysis.

Quality control of blood plasma for mass-spectrometry proteomic research

The paper establishes a targeted method to assess plasma sample quality using hemolysis markers and proposes integrating hemolysis assessment into standard MRM analysis.

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis

The paper introduces a 'mono-mix' strategy to improve proteomic analysis of cross-kingdom microbial symbiosis by addressing detection biases in coculture.

Single-cell proteomics of Arabidopsis leaf mesophyll identifies drought stress-related proteins

This study applies single-cell proteomics to Arabidopsis leaf mesophyll cells to identify drought stress-related proteins and changes in protein networks.

Serial enrichment based quantitative proteomics enables deep and multiplexed profiling of post-translational modifications

This paper introduces a serial enrichment workflow for quantitative proteomics that enables deep and multiplexed profiling of multiple post-translational modifications from a single sample.

A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs

The paper introduces a new detailed mass offset search method in MSFragger to improve the interpretation of complex post-translational modifications.

If the shoe fits? -- technical nuances of plasma proteomic workflows in clinical and preclinical contexts

The paper benchmarks plasma proteomic workflows across species and methods, showing workflow choice significantly impacts detected proteins and depth.

Interface-Resolved Proteomics of Cell-Cell Membranes Reveals Early Spatial Polarity in a Vertebrate Embryo

The paper develops an interface-resolved proteomics method to analyze cell-cell membrane contacts in Xenopus embryos, revealing molecular polarity at early developmental stages.

Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells

The paper introduces in-cell LiP-MS to study protein structural changes and biomolecular condensates in live human cells, revealing structural alterations under stress and validating them with microscopy.

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments.

quantms-rescoring improves proteomics analysis by integrating multiple search engines and machine learning, increasing identified spectra and quantifying more phosphorylated peptides and modification sites.

The Demodifier: a tool for screening modification-induced alternate peptide taxonomy in palaeoproteomics

The Demodifier identifies modification-induced errors in peptide taxonomy in palaeoproteomics, revealing they are more common than previously thought.

Atlas of lysine acetylation in the mouse

The paper presents a comprehensive atlas of lysine acetylation in the mouse, identifying 17,952 sites across 15 tissues and highlighting shared and tissue-specific acetylation events.

Higher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer

Orbitrap Astral Zoom upgrades enable 270 Hz DIA scanning, identifying 7184 protein groups at 500 samples/day and >12,000 proteins from fractionated HEK293 in 2.7 h.

Benchmarking Peptide Spectral Library Search

The paper benchmarks peptide spectral library search methods using a new dataset, finding poor recall (~70%) and varying performance across scoring functions and preprocessing scenarios.

Multiplexed Data-Independent Acquisition (mDIA) to Profile Extracellular Vesicle Proteomes

This study establishes a robust mDIA pipeline for EV proteomics, showing library-based DIA outperforms other methods and reveals IDH1 mutation effects on EV proteomes in cholangiocarcinoma.