ArticleNature methods2017
Building ProteomeTools based on a complete synthetic human proteome.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
110 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics.Nature methods · 2026Article
- InstaNovo-P: a de novo peptide sequencing model for phosphoproteomics.Nature communications · 2026Article
- Cross-domain transfer learning from peptides to metabolites using a multi-property fine-tuned LLM.Bioinformatics (Oxford, England) · 2026Article
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.Analytical chemistry · 2026Article
- Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction.bioRxiv : the preprint server for biology · 2026Article
- Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides.Molecular & cellular proteomics : MCP · 2026Article
- Generation of peptide detectability datasets from single DIA experiment for prediction model fine-tuning.Bioinformatics advances · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.Communications chemistry · 2025Article
- Artificial Intelligence and the Evolving Landscape of Immunopeptidomics.Proteomics. Clinical applications · 2025Review
- Integrated fibre-specific methylome and proteome profiling of human skeletal muscle across males and females with fibre-type deconvolution.Skeletal muscle · 2025Article
- Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.Nature communications · 2025Article
- FastSpel: A Method for Fast Spectral Library Generation.Journal of proteome research · 2025Article
- Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures.Nature communications · 2025Article
- To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry.Journal of proteome research · 2025Article
- Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models.Proteomics · 2025Review
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments.Nature machine intelligence · 2025Article
- Comparison of the Human Plasma Peptides from the Fit of Fragmentation Spectra versus Accurate Monoisotopic Precursor Mass.ACS omega · 2025Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
24 authors.
Funding
Abstract
We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography-tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.