ArticleJournal of proteome research2018
Proteome-Wide Evaluation of Two Common Protein Quantification Methods.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 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
100 citing papers in PubMed, 201 citations in OpenAlex.
- Diabetic Polyneuropathy Patients Exhibit an Altered Skeletal Muscle Proteome Phenotype.Proteomics. Clinical applications · 2026Article
- Herpes simplex virus pUL56 abolishes neuronal activity by removing voltage-gated ion channels from the plasma membrane.Science advances · 2026Article
- Transcending genome-wide association studies to create useful multi-omic views of glaucoma.Progress in retinal and eye research · 2026Review
- Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.Journal of the American Society for Mass Spectrometry · 2026Article
- Proteomic analysis of the pyrenoid-traversing membranes of Chlamydomonas reinhardtii reveals novel components.The New phytologist · 2026Article
- optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference.Bioinformatics advances · 2026Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- Astrocyte FABP7 Modulates Seizure Activity-Dependent Protein Expression in Mouse Brain.Neuroglia (Basel, Switzerland) · 2025Article
- Quantification of parathyroid hormone in high-purity materials by two isotope dilution mass spectrometry methods.Analytical and bioanalytical chemistry · 2025Article
- Short and long-term effects on the thyroid proteome after 131I exposure.Radiation protection dosimetry · 2025Article
- Proteomic analysis of the pyrenoid-traversing membranes ofbioRxiv : the preprint server for biology · 2025Article
- Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.Briefings in bioinformatics · 2025Article
- ARF6 as a Novel Activator of HIF-2α in Pulmonary Arterial Hypertension.American journal of respiratory cell and molecular biology · 2025Article
- Long-term CSF responses in adult patients with spinal muscular atrophy type 2 or 3 on treatment with nusinersen.Journal of neurology · 2025Article
- Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics.Nature communications · 2025Article
- Data acquisition approaches for single cell proteomics.Proteomics · 2025Review
- Pleiotropic tumor suppressive functions of PTEN missense mutations during gliomagenesis.iScience · 2024Article
- Stem Cell-Associated Proteins and Extracellular Matrix Composition of the Human Atrioventricular Junction.Cells · 2024Article
40 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
4 authors at 1 institution in 1 country.
Funding
Abstract
Proteomics experiments commonly aim to estimate and detect differential abundance across all expressed proteins. Within this experimental design, some of the most challenging measurements are small fold changes for lower abundance proteins. While bottom-up proteomics methods are approaching comprehensive coverage of even complex eukaryotic proteomes, failing to reliably quantify lower abundance proteins can limit the precision and reach of experiments to much less than the identified-let alone total-proteome. Here we test the ability of two common methods, a tandem mass tagging (TMT) method and a label-free quantitation method (LFQ), to achieve comprehensive quantitative coverage by benchmarking their capacity to measure 3 different levels of change (3-, 2-, and 1.5-fold) across an entire data set. Both methods achieved comparably accurate estimates for all 3-fold-changes. However, the TMT method detected changes that reached statistical significance three times more often due to higher precision and fewer missing values. These findings highlight the importance of refining proteome quantitation methods to bring the number of usefully quantified proteins into closer agreement with the number of total quantified proteins.
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.