ArticleMolecular & cellular proteomics : MCP2015
Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.
Article in Molecular & cellular proteomics : MCP, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT02570698 (Collection and Characterization of Premature Infants Feces for Identification of Factors Contributing to Skin Irritation), which is not on this map. Cited by 666 papers.
What it found
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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.
Collection and Characterization of Premature Infants Feces for Identification of Factors Contributing to Skin Irritation
Who cites it
666 citing papers in PubMed.
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- Structure-guided parameter optimization of feature-based molecular networking for DIA-HRMS screening of antihistamines in cosmetics.Analytical and bioanalytical chemistry · 2026Article
- Powassan Virus NS5 Antagonizes TYK2-Mediated Immune Signaling Pathways.bioRxiv : the preprint server for biology · 2026Article
- Nuclear remodeling and optimal migration emerge early, and constriction-passage progressively improves during hematopoietic stem cells to neutrophils differentiation.bioRxiv : the preprint server for biology · 2026Article
- Dynamic Atlas and Energy Metabolism Adaptation of the Liver Proteome During a 24 h Cycle inBiomolecules · 2026Article
- Proteome analyses reveal endoplasmic reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture.G3 (Bethesda, Md.) · 2026Article
- Urinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma.EMBO molecular medicine · 2026Article
606 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)(1)-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling.
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