ArticleNature communications2021
IceR improves proteome coverage and data completeness in global and single-cell proteomics.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed.
- What Are the Practical Applications of Single-Cell Proteomics?Proteomes · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Alternative Ion-Pairing Modifiers Should Be Investigated in Low-Input and Single-Cell Proteomics.Journal of proteome research · 2025Article
- Hyperactivity of subicular parvalbumin interneurons drives early amyloid pathology and cognitive deficits in Alzheimer's disease.Molecular psychiatry · 2025Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.Proteomics · 2025Article
- NET Proteomic Profiling Reveals New Pathways Potentially Implicated in Dendritic Cell-Mediated Inflammation in DADA2 Patients.Journal of clinical immunology · 2025Article
- Mass Spectrometry-based Solutions for Single-cell Proteomics.Genomics, proteomics & bioinformatics · 2025Review
- Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.Scientific reports · 2025Article
- Value of Label-Free Ubiquitin-Proteomic Analysis on Defining the Protective Mechanism of Valsartan against Doxorubicin-Induced Heart Failure.Current cancer drug targets · 2025Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Acetic acid is a superior ion pairing modifier for sub-nanogram and single cell proteomics.bioRxiv : the preprint server for biology · 2024Article
- Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.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
- What's new in single-cell proteomics.Current opinion in biotechnology · 2024Review
- A Multiplexed Single-Cell Proteomic Workflow Applicable to Drug Treatment Studies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A High-Sensitivity Low-Nanoflow LC-MS Configuration for High-Throughput Sample-Limited Proteomics.Analytical chemistry · 2023Article
- Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRASJournal of proteome research · 2023Article
- An integrated method for single cell proteomics with simultaneous measurements of intracellular drug concentration implicates new mechanisms for adaptation to KRASbioRxiv : the preprint server for biology · 2023Article
- Metabolomic, proteomic and single cell proteomic analysis of cancer cells treated with the KRASbioRxiv : the preprint server for biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly quantification workflow that combines high identification rates of data-dependent acquisition with low missing value rates similar to data-independent acquisition. Specifically, IceR uses ion current information for a hybrid peptide identification propagation approach with superior quantification precision, accuracy, reliability and data completeness compared to other quantitative workflows. Applied to plasma and single-cell proteomics data, IceR enhanced the number of reliably quantified proteins, improved discriminability between single-cell populations, and allowed reconstruction of a developmental trajectory. IceR will be useful to improve performance of large scale global as well as low-input proteomics applications, facilitated by its availability as an easy-to-use R-package.
Indexed as
Identifiers
What OpenQuestion holds
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.