ArticleNature methods2011
Rapid empirical discovery of optimal peptides for targeted proteomics.
Article in Nature methods, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Prioritizing peptides for targeted mass spectrometry experiments using deep learning.bioRxiv : the preprint server for biology · 2026Article
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
- Uniquome: Construction and decoding of a novel proteomic atlas that contains new peptide entities.Computational and structural biotechnology journal · 2025Article
- Hybrid Quadrupole Mass Filter-Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.Journal of proteome research · 2024Article
- Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.bioRxiv : the preprint server for biology · 2024Article
- Article
- Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers.International journal of molecular sciences · 2021Article
- Novel Corneal Protein Biomarker Candidates Reveal Iron Metabolic Disturbance in High Myopia Eyes.Frontiers in cell and developmental biology · 2021Article
- The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.Mass spectrometry reviews · 2020Review
- The production of isoprene from cellulose using recombinant Clostridium cellulolyticum strains expressing isoprene synthase.MicrobiologyOpen · 2020Article
- Article
- Differential Roles of the Thylakoid Lumenal Deg Protease Homologs in Chloroplast Proteostasis.Plant physiology · 2018Article
- Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.Journal of proteomics · 2018Review
- Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.Molecular systems biology · 2018Review
- Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics.Synthetic and systems biotechnology · 2018Review
- PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.Nature methods · 2017Article
- An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases.Molecular & cellular proteomics : MCP · 2017Article
- Systems Biology-Derived Discoveries of Intrinsic Clocks.Frontiers in neurology · 2017Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We report a method for high-throughput, cost-efficient empirical discovery of optimal proteotypic peptides and fragment ions for targeted proteomics applications using in vitro-synthesized proteins. We demonstrate the approach using human transcription factors, which are typically difficult, low-abundance targets and empirically derived proteotypic peptides for 98% of the target proteins. We show that targeted proteomic assays developed using our approach facilitate robust in vivo quantification of human transcription factors.
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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.