ArticleJournal of proteome research2014
Intelligent data acquisition blends targeted and discovery methods.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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.
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Who cites it
29 citing papers in PubMed.
- Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics.Nature communications · 2025Article
- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 2025Article
- Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags.Journal of proteome research · 2025Article
- TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.Journal of proteome research · 2025Article
- IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection.Journal of the American Society for Mass Spectrometry · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing.Journal of proteome research · 2024Article
- IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.bioRxiv : the preprint server for biology · 2024Article
- Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.Journal of proteome research · 2023Article
- Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching.Analytical chemistry · 2023Article
- Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.Nature methods · 2023Article
- Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression.Nature communications · 2023Article
- FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts.Nature communications · 2022Article
- Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview.Metabolites · 2021Review
- Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.Journal of proteome research · 2020Article
- Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics.Journal of proteome research · 2020Article
- Accelerating Lipidomic Method Development throughAnalytical chemistry · 2019Article
- MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides.Molecular & cellular proteomics : MCP · 2019Article
- Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows.Journal of proteome research · 2019Article
- Building ProteomeTools based on a complete synthetic human proteome.Nature methods · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
A mass spectrometry (MS) method is described here that can reproducibly identify hundreds of peptides across multiple experiments. The method uses intelligent data acquisition to precisely target peptides while simultaneously identifying thousands of other, nontargeted peptides in a single nano-LC-MS/MS experiment. We introduce an online peptide elution order alignment algorithm that targets peptides based on their relative elution order, eliminating the need for retention-time-based scheduling. We have applied this method to target 500 mouse peptides across six technical replicate nano-LC-MS/MS experiments and were able to identify 440 of these in all six, compared with only 256 peptides using data-dependent acquisition (DDA). A total of 3757 other peptides were also identified within the same experiment, illustrating that this hybrid method does not eliminate the novel discovery advantages of DDA. The method was also tested on a set of mice in biological quadruplicate and increased the number of identified target peptides in all four mice by over 80% (826 vs 459) compared with the standard DDA method. We envision real-time data analysis as a powerful tool to improve the quality and reproducibility of proteomic data sets.
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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.