ArticleJournal of proteome research2014
Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.
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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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
29 citing papers in PubMed.
- mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry.BMC bioinformatics · 2026Article
- Standardized Workflow for Mass-Spectrometry-Based Single-Cell Proteomics Data Processing and Analysis Using the scp Package.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The Biomarkers in Extreme Longevity: Insights Gained from Metabolomics and Proteomics.International journal of medical sciences · 2024Review
- High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation.Nature protocols · 2023Review
- Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification.Analytical chemistry · 2021Article
- Robust Summarization and Inference in Proteome-wide Label-free Quantification.Molecular & cellular proteomics : MCP · 2020Article
- MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts.Mass spectrometry reviews · 2019Review
- Modeling Corticosteroid Pharmacogenomics and Proteomics in Rat Liver.The Journal of pharmacology and experimental therapeutics · 2018Article
- Proteomic Analysis of Charcoal-Stripped Fetal Bovine Serum Reveals Changes in the Insulin-like Growth Factor Signaling Pathway.Journal of proteome research · 2018Article
- Receptor/gene/protein-mediated signaling connects methylprednisolone exposure to metabolic and immune-related pharmacodynamic actions in liver.Journal of pharmacokinetics and pharmacodynamics · 2018Article
- IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- GPR56/ADGRG1 regulates development and maintenance of peripheral myelin.The Journal of experimental medicine · 2018Article
- An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts.Journal of proteome research · 2017Article
- Comparative Proteomic Analysis of the Mitochondria-associated ER Membrane (MAM) in a Long-term Type 2 Diabetic Rodent Model.Scientific reports · 2017Article
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.Journal of proteomics · 2017Article
- Quantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients.Proteomics. Clinical applications · 2017Article
- Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods.Molecular bioSystems · 2016Article
- Large-Scale, Ion-Current-Based Proteomic Investigation of the Rat Striatal Proteome in a Model of Short- and Long-Term Cocaine Withdrawal.Journal of proteome research · 2016Article
- Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine.Proteomics · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.
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