ArticleJournal of the American Society for Mass Spectrometry2021
HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments.
Article in Journal of the American Society for Mass Spectrometry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 2025Article
- Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer.Journal of proteome research · 2025Article
- Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.Journal of the American Society for Mass Spectrometry · 2024Article
- Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference.Nature communications · 2024Article
- A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments.Nature methods · 2024Article
- A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics.Molecular & cellular proteomics : MCP · 2024Article
- Deep Proteomic Compound Profiling with the Orbitrap Ascend Tribrid Mass Spectrometer Using Tandem Mass Tags and Real-Time Search.Analytical chemistry · 2023Article
- Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.Journal of proteome research · 2023Article
- IsobaricQuant enables cross-platform quantification, visualization, and filtering of isobarically-labeled peptides.Proteomics · 2022Article
- Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing.Proteomics · 2022Article
- Assessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard.Proteomics · 2022Article
- Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics.Analytical chemistry · 2022Review
- A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies.Journal of proteome research · 2021Article
- A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation.Journal of the American Society for Mass Spectrometry · 2021Article
- Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies.Analytical chemistry · 2021Article
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3 authors.
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Abstract
Isobaric tagging is a powerful strategy for global proteome profiling. A caveat of isobaric-tag-based quantification is "interference", which may be caused by coeluting peptides that are coisolated, cofragmented, and coanalyzed, thereby confounding quantitative accuracy. Here, we present a two-proteome standard that challenges the mass spectrometer to measure a range of protein abundance ratios in a background of potential interference. The HYpro16 standard consists of tandem mass tag (TMT) pro16-labeled human peptides at a 1:1 ratio across all channels into which is spiked TMTpro16-labeled yeast peptides in triplicate at 20:1, 10:1, 4:1, and 2:1 ratios. We showcase the HYpro16 standard by (1) altering the MS2 isolation window width and (2) examining different data acquisition methods (hrMS2, SPS-MS3, RTS-MS3). Our data illustrate that wider isolation widths moderately increase the TMT signal, the benefits of which are offset by decreased ratio accuracy. We also show that using real-time database searching (RTS)-MS3 resulted in the most accurate ratios. Additionally, the number of quantified yeast proteins using RTS-MS3 approaches that of hrMS2 when using a yeast-specific database for real-time searching. In short, this quality control standard allows for the assessment of multiple quantitative measurements within a single run, which can be compared across instruments to benchmark and track performance.
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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.