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Beyond the Static Caliper: Dynamical Translocases and the Mathematical Imperative for Single-Molecule Proteomics www.biorxiv.org/cont... --- #proteomics #prot-preprint

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X-PAIR: an ultrafast multitask framework for proteome-scale reconstruction of PPI networks and partner-specific interfaces from sequence www.biorxiv.org/cont... --- #proteomics #prot-preprint

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AlphaFold Database expands to proteome-scale quaternary structures www.researchsquare.c... --- #proteomics #prot-preprint

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Formic Acid Enhanced Single-Pot Sample Preparation to Improve Identification Coverage of Membrane Proteome of Laser Capture Microdissected Tissue Sections pubs.acs.org/doi/10.... --- #proteomics #prot-paper

The Metaproteomics Initiative: five years of community-driven progress link.springer.com/ar... --- #proteomics #prot-paper

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The need for standardization and improved open (meta)data practices in metaproteomics link.springer.com/ar... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 23/07/2026

LABEL-FREE TARGETED PROTEOMICS DATA ANALYSIS WORKFLOW SELECTION – BENCHMARKING AI-BASED AND DATA-DRIVEN APPROACHES www.mcponline.org/ar... --- #proteomics #prot-paper

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Improved Protein Identification in Shotgun Proteomics with a Group-Level Extension of the LPGF Model pubs.acs.org/doi/10.... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 23/07/2026

Hidden proteins encoded by non-canonical open reading frames: A review www.sciencedirect.co... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 23/07/2026

SoftHybrid: A Hybrid Imputation Algorithm Optimized for Single-Cell Proteomics Data pubs.acs.org/doi/10.... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 22/07/2026

Remember, once in a Blue Moon, to visit Pastel BioScience's resource pages ... t.ly/EP3hr to see updated list of new #proteomics software packages (153) in 2025 &, t.ly/Mlk39 for Conferences/Symposia/Webinars etc (11) already available in 2026 --- #proteomics #prot-other

PastelBio @pastelbio.bsky.social · 22/07/2026

TraianProt: a user-friendly R shiny application for wide format... arxiv.org/abs/2412.1... Link that works for shiny app --- samueldelacamara.shi... --- #proteomics #prot-preprint

PastelBio @pastelbio.bsky.social · 22/07/2026

SPgen: Proteome-wide Spatial Proteomics generation using multi-modality foundation models www.biorxiv.org/cont... --- #proteomics #prot-preprint

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PastelBio @pastelbio.bsky.social · 21/07/2026

Estimating animal species from blood using in-gel digestion peptide mass fingerprinting pubs.rsc.org/ay/arti... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 21/07/2026

ProtSyntax: a protein large language model for decoding post-translational modification syntax and function www.biorxiv.org/cont... --- #proteomics #prot-preprint

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PastelBio @pastelbio.bsky.social · 21/07/2026

Plasma proteome profiling identified biomarkers for the differential diagnosis and molecular staging of neurodegenerative dementias www.nature.com/artic... --- #proteomics #prot-paper

A targeted mass-spectrometry plasma proteome for simultaneous multi-disease screening www.biorxiv.org/cont... --- #proteomics #prot-preprint

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Age-dependent Structural Reorganization of the Human Plasma Proteome www.biorxiv.org/cont... --- #proteomics #prot-preprint

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MSstatsQC-ML: A Supervised Machine Learning Approach to Monitor System Suitability and Quality Control in Mass Spectrometry-Based Proteomics pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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PastelBio @pastelbio.bsky.social · 19/07/2026

Collection on Forensic Proteomics pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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ProLM: a plasma proteomics pretrained model for the general population www.nature.com/artic... --- #proteomics #prot-paper

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PastelBio @pastelbio.bsky.social · 19/07/2026

Enrichment-Free Deep Proteomics Enables Proteome-Scale Analysis of Methionine Oxidation academic.oup.com/dna... --- #proteomics #prot-paper

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PastelBio @pastelbio.bsky.social · 19/07/2026

‘If the shoe fits?’ – Benchmarking plasma proteomic sample-preparation workflows across human and rat biofluids www.mcponline.org/ar... --- #proteomics #prot-paper

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Improved Protein Identification in Native Ambient Mass Spectrometry by the Integration of Proton Transfer Charge Reduction and Higher-Energy Collision Dissociation (PTCR-HCD MS3) pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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High-Throughput Single-Cell Proteomics Enabled by Integrating nPOP Workflow with Quantitative Hyperplexing pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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ARGpredict: A web server to predict arginylation events in a protein www.sciencedirect.co... --- #proteomics #prot-paper

Tandem MICROFASP Method-Enabled High-Sensitivity In Vivo Cross-Linking Mass Spectrometry Analysis of Low-Cell-Number Samples without Enrichment pubs.acs.org/doi/10.... --- #proteomics #prot-paper

A Robust and Generalizable Low-Input Spatial Proteomics Workflow Enabling Deep Proteome Coverage www.biorxiv.org/cont... --- #proteomics #prot-preprint

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PeptiVerse: A unified platform for therapeutic peptide property prediction www.nature.com/artic... --- #proteomics #prot-paper

Evaluating DIA LiP-MS Analysis Workflows with a Hybrid LiP Proteome Benchmark pubs.acs.org/doi/10.... --- #proteomics #prot-paper

Top-Down versus Bottom-Up Proteomics in Highly Sensitive LC-MS-Based Profiling of Limited Samples pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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MSstatsBioNet: Integrating Statistical Analyses with Prior Knowledge Biomolecular Networks for Quantitative Proteomics and Phosphoproteomics www.biorxiv.org/cont... --- #proteomics #prot-preprint

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News in Proteomics Research blog post | Preprinted data featured at SCP2026 day 2! proteomicsnews.blogs... --- #proteomics #prot-other

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NicheProt: Cell-type-resolved proteomics of tissue compartments www.science.org/doi/... --- #proteomics #prot-paper

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High-throughput monitoring of in vitro enzymatic reactions using probe electrospray ionization-mass spectrometry link.springer.com/ar... --- #proteomics #prot-paper

ProteoMeter: a pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level academic.oup.com/nar... --- #proteomics #prot-paper

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MS-Compatible Hydrophobic Interaction Chromatography of Intact Proteins Using Long-Ligand Stationary Phases www.sciencedirect.co... --- #proteomics #prot-paper

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News in Proteomics Research blog post | Preprinted data featured in Day 1 at SCP2026! proteomicsnews.blogs... --- #proteomics #prot-other

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Analysis and Annotation of c-Type Ions in Peptide Mass Spectral Libraries pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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Instrument–Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods pubs.acs.org/doi/10.... --- #proteomics #prot-paper

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HighDB: a structure-annotated cyclic peptide database for comparative analysis, template retrieval, and design-oriented applications link.springer.com/ar... --- #proteomics #prot-paper

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A fast high-throughput logP estimation method for peptide molecules based on liquid chromatography-mass spectrometry method link.springer.com/ar... --- #proteomics #prot-paper

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Proteoform Detection across 17000 Single Nuclei from Differentiating Skin Keratinocytes www.mcponline.org/ar... --- #proteomics #prot-paper

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Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking www.biorxiv.org/cont... --- #proteomics #prot-preprint

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Molecular profiling of the single-cell proteome via gel electrophoresis and 3D single-molecule imaging www.nature.com/artic... --- #proteomics #prot-paper

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Understanding Mass Spectrometry: From Ion Generation to Spectral Interpretation analyticalsciencejou... --- #proteomics #prot-paper

PastelBio @pastelbio.bsky.social · 13/07/2026

News in Proteomics Research blog post | It's finally here! SCP2026! proteomicsnews.blogs... --- #proteomics #prot-other

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Proteoform-specific enrichment of phosphopeptide isomers by polymer-based synthetic receptors www.nature.com/artic... --- #proteomics #prot-paper

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PastelBio @pastelbio.bsky.social · 13/07/2026

News in Proteomics Research blog post | It's official! THE Proteomics Show live at the British Mass Spec Society! proteomicsnews.blogs... --- #proteomics #prot-other