ArticleNature methods2016
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 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.
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Who cites it
93 citing papers in PubMed, 201 citations in OpenAlex.
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- Depletion-dependent activity-based protein profiling using SWATH/DIA-MS detects serine hydrolase lipid remodeling in lung adenocarcinoma progression.Nature communications · 2025Article
- Proteomic Insights into IgA Nephropathy: A Comprehensive Analysis of Differentially Expressed Proteins in the Kidney.ACS omega · 2025Article
- Proteomics appending a complementary dimension to precision oncotherapy.Computational and structural biotechnology journal · 2024Review
- Cross-Run Hybrid Features Improve the Identification of Data-Independent Acquisition Proteomics.ACS omega · 2024Article
- Proteome-wide copy-number estimation from transcriptomics.Molecular systems biology · 2024Article
- SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics.Interdisciplinary sciences, computational life sciences · 2024Article
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
- Targeting low levels of MIF expression as a potential therapeutic strategy for ALS.Cell reports. Medicine · 2024Article
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.Cell host & microbe · 2024Article
- Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment.Communications biology · 2023Article
- Article
- Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.Journal of proteome research · 2023Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 5 institutions in 4 countries.
Funding
Abstract
Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics 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.