ArticleACS omega2021
Benchmarking Quantitative Performance in Label-Free Proteomics.
Article in ACS omega, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.International journal of molecular sciences · 2025Pooled it
- Comparative analysis of neuronal proteolytic pathways reveals neuron-specific and sub-compartmental-specific capacities with aging.Cellular and molecular life sciences : CMLS · 2026Article
- Evaluating Synthetic Cyber Deception Strategies Under Uncertainty via Game Theory Approach: Linking Information Leakage and Game Outcomes in Cyber Deception.Sensors (Basel, Switzerland) · 2026Article
- A proteome-wide dependency map of protein interaction motifs.Nature structural & molecular biology · 2026Article
- Nitric oxide required for transition to slower hepatic protein synthesis rates during long-term caloric restriction.The Journal of clinical investigation · 2026Article
- Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity.The EMBO journal · 2025Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- A cellular model of TDP-43 induces phosphorylated TDP-43 aggregation with distinct changes in solubility and autophagy dysregulation.The FEBS journal · 2025Article
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- SAPrIm 2.0: a semi-automated protocol for mid-throughput soluble HLA immunopeptidomics.Frontiers in immunology · 2025Article
- Article
- PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks.Bioinformatics (Oxford, England) · 2024Article
- Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics.Molecular & cellular proteomics : MCP · 2024Review
- Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference.Nature communications · 2024Article
- A Mass Spectrometry Strategy for Protein Quantification Based on the Differential Alkylation of Cysteines Using Iodoacetamide and Acrylamide.International journal of molecular sciences · 2024Article
- Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience.Proteomes · 2024Article
- Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics.Journal of proteome research · 2024Article
- Application of N-Terminal Labeling Methods Provide Novel Insights into Endoproteolysis of the Prion ProteinACS chemical neuroscience · 2024Article
- Proteomic Identification and Label-Free Quantification of Proteins Implicated in Neurite and Spine Formation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Proteomic Alteration in the Progression of Multiple Myeloma: A Comprehensive Review.Diagnostics (Basel, Switzerland) · 2023Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Previous benchmarking studies have demonstrated the importance of instrument acquisition methodology and statistical analysis on quantitative performance in label-free proteomics. However, the effects of these parameters in combination with replicate number and false discovery rate (FDR) corrections are not known. Using a benchmarking standard, we systematically evaluated the combined impact of acquisition methodology, replicate number, statistical approach, and FDR corrections. These analyses reveal a complex interaction between these parameters that greatly impacts the quantitative fidelity of protein- and peptide-level quantification. At a high replicate number (
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.