A Mass Spectrometry-Based Proteomics Workflow for Concurrent Profiling https://link.springer.com/protocol/10.1007/978-1-0716-4574-1_17

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#proteomics #prot-paper

Precision Medicine and the Human Proteome in Disease, Diagnostics and Translation: Current Status and Future Prospects - Abstract - Europe PMC https://europepmc.org/article/PMC/PMC12109353?source=rss#free-full-text

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#proteomics #prot-paper

TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification https://pubs.acs.org/doi/10.1021/acs.analchem.4c06627

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#proteomics #prot-paper

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets https://www.cell.com/cancer-cell/abstract/S1535-6108(25)00212-0

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#proteomics #prot-paper

Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry https://www.biorxiv.org/content/10.1101/2025.05.26.656138v1.full.pdf+html

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#proteomics #prot-preprint

Deep palaeoproteomic profiling of archaeological human brains https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0324246

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#proteomics #prot-paper

DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra https://arxiv.org/abs/2502.09571

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#proteomics #prot-preprint

Deconvolution of multiplexed peptidoform mass spectra enables high-resolution profiling of complex protein modification patterns https://www.biorxiv.org/content/10.1101/2025.05.24.655917v1.full.pdf+html

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#proteomics #prot-preprint

Evaluation of PE5 entries on the Human Proteome Project Target List https://chemrxiv.org/engage/chemrxiv/article-details/683155b03ba0887c33968355

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#proteomics #prot-preprint

A Method for Comparing Proteins Measured in Serum and Plasma by Olink® Proximity Extension Assay https://www.sciencedirect.com/science/article/pii/S1535947625000994?dgcid=rss_sd_all

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#proteomics #prot-paper

Increasing mass spectrometry throughput using time-encoded sample multiplexing https://www.biorxiv.org/content/10.1101/2025.05.22.655515v1

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#proteomics #prot-preprint

Sequence-Only Prediction of Binding Affinity Changes: A Robust and Interpretable Model for Antibody Engineering https://arxiv.org/abs/2505.20301

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#proteomics #prot-preprint

Prot2Token: A Unified Framework for Protein Modeling via... https://arxiv.org/abs/2505.20589

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#proteomics #prot-preprint

PDFBench: A Benchmark for De novo Protein Design from Function https://arxiv.org/abs/2505.20346

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#proteomics #prot-preprint

TumorHoPe2: An updated database for Tumor Homing Peptides https://arxiv.org/abs/2505.20913

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#proteomics #prot-preprint

Guide your favorite protein sequence generative model https://arxiv.org/abs/2505.04823

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#proteomics #prot-preprint

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology https://www.embopress.org/doi/full/10.1038/s44320-025-00121-5

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#proteomics #prot-paper

JMod: Joint modeling of mass spectra for empowering multiplexed DIA proteomics https://www.biorxiv.org/content/10.1101/2025.05.22.655512v1.full.pdf+html

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#proteomics #prot-preprint

Transformers in Protein: A Survey https://arxiv.org/abs/2505.20098

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#proteomics #prot-preprint

News in Proteomics Research blog post | Increase your multiplexing by adding the time dimension (and more nanoLC columns!) https://proteomicsnews.blogspot.com/2025/05/increase-your-multiplexing-by-adding.html

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#proteomics #prot-other