ArticleMolecular & cellular proteomics : MCP2023
Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.
Article in Molecular & cellular proteomics : MCP, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- Peptides as integrative modulators for clinical prognosis and targeted therapy in pancreatic cancer.Discover oncology · 2026Review
- Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1.Nature communications · 2026Article
- JUMPlion improves quantitative DIA proteomics through ion-level recovery of missing values.bioRxiv : the preprint server for biology · 2026Article
- Proteome dynamics during establishment of California grunion (Leuresthes tenuis) cell lines.BMC biology · 2026Article
- Proteomic profiling of human omental and subcutaneous adipose tissue in individuals with a broad range of BMI.Scientific data · 2026Article
- Proteomic Analysis of Cerebrospinal Fluid from Severe COVID-19 Patients Reveals Prognostic Biomarkers Associated with Disease Outcome.Proteomics. Clinical applications · 2026Article
- Proteoforms as the true units of physiological function.European journal of applied physiology · 2026Review
- Single-cell spatial proteomics maps human liver zonation patterns and their vulnerability to disruption in tissue architecture.Nature metabolism · 2026Article
- Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.Journal of the American Society for Mass Spectrometry · 2026Article
- Clonal haematopoiesis of indeterminate potential and mortality in coronary artery disease.European heart journal · 2026Article
- Proteomic Profiling of Human Omental and Subcutaneous Adipose Tissue in Individuals with a Broad Range of BMI.bioRxiv : the preprint server for biology · 2026Article
- Autophagy selectively clears ER in TNF-α-induced muscle atrophy.Autophagy reports · 2026Article
- LimROTS: a hybrid method integrating empirical Bayes and reproducibility-optimized statistics for robust differential expression analysis.Bioinformatics (Oxford, England) · 2025Article
- Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates.Proteomics · 2025Review
- Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.Nature communications · 2025Article
- Advances in ciliary proteomics - towards cracking the hidden proteome code of cilia.Journal of cell science · 2025Review
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Recent advances in mass spectrometry-based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks in the bioinformatics pipeline. Although peptide identification is already scalable, most label-free quantification (LFQ) algorithms scale quadratic or cubic with the sample numbers, which may even preclude the analysis of large-scale data. Here we introduce directLFQ, a ratio-based approach for sample normalization and the calculation of protein intensities. It estimates quantities via aligning samples and ion traces by shifting them on top of each other in logarithmic space. Importantly, directLFQ scales linearly with the number of samples, allowing analyses of large studies to finish in minutes instead of days or months. We quantify 10,000 proteomes in 10 min and 100,000 proteomes in less than 2 h, a 1000-fold faster than some implementations of the popular LFQ algorithm MaxLFQ. In-depth characterization of directLFQ reveals excellent normalization properties and benchmark results, comparing favorably to MaxLFQ for both data-dependent acquisition and data-independent acquisition. In addition, directLFQ provides normalized peptide intensity estimates for peptide-level comparisons. It is an important part of an overall quantitative proteomic pipeline that also needs to include high sensitive statistical analysis leading to proteoform resolution. Available as an open-source Python package and a graphical user interface with a one-click installer, it can be used in the AlphaPept ecosystem as well as downstream of most common computational proteomics pipelines.
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