ReviewComputational and structural biotechnology journal2022
Perspectives for better batch effect correction in mass-spectrometry-based proteomics.
Review in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- GlycoDiveR: A Modular R Framework to Analyze and Visualize Highly Dimensional Glycoproteomics Data.ACS measurement science au · 2026Article
- Single-cell proteomic landscape of the developing human brain.Nature biotechnology · 2026Article
- Plasma Proteomic Profiling Was Used to Discover a Biochemical Recurrence Prediction Model for Prostate Cancer.Molecular & cellular proteomics : MCP · 2026Article
- GlycoDiveR: a modular R framework to analyze and visualize highly dimensional glycoproteomics data.bioRxiv : the preprint server for biology · 2026Article
- Optimising the choice of normalisation method for use in machine-learning classification of human blood plasma ambient ionisation mass spectra.International journal of mass spectrometry · 2026Article
- A novel batch effect correction framework for robust integration of high-variance data via a global-information virtual reference batch.Frontiers in microbiology · 2026Article
- Benchmarking ensemble and deep learning models for drought-responsive gene prioritisation in rice using multi-omics data.PloS one · 2026Article
- Immune-Based Biomarkers as Predictors of Mortality in ECMO Therapy for Severe COVID-19 ARDS: Insights from a Retrospective Study.International journal of molecular sciences · 2025Observational
- Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology.bioRxiv : the preprint server for biology · 2025Article
- PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder.Bioinformatics (Oxford, England) · 2025Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- NPM: latent batch effects correction of omics data by nearest-pair matching.Bioinformatics (Oxford, England) · 2025Article
- Methylation profiling in neuropathological tumors diagnosis: a comprehensive review.Frontiers in oncology · 2025Review
- Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison.Briefings in bioinformatics · 2024Article
- Assessing and mitigating batch effects in large-scale omics studies.Genome biology · 2024Review
- Proteomics of the heart.Physiological reviews · 2024Review
- Article
- A non-invasive method for concurrent detection of multiple early-stage cancers in women.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mass-spectrometry-based proteomics presents some unique challenges for batch effect correction. Batch effects are technical sources of variation, can confound analysis and usually non-biological in nature. As proteomic analysis involves several stages of data transformation from spectra to protein, the decision on when and what to apply batch correction on is often unclear. Here, we explore several relevant issues pertinent to batch effect correct considerations. The first involves applications of batch effect correction requiring prior knowledge on batch factors and exploring data to uncover new/unknown batch factors. The second considers recent literature that suggests there is no single best batch effect correction algorithm---i.e., instead of a best approach, one may instead ask, what is a suitable approach. The third section considers issues of batch effect detection. And finally, we look at potential developments for proteomic-specific batch effect correction methods and how to do better functional evaluations on batch corrected data.
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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.