ArticleJournal of proteome research2021
Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Mitochondrial Proteomes in Neural Cells: A Systematic Review.Biomolecules · 2023Pooled it
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- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental.bioRxiv : the preprint server for biology · 2026Article
- Rubicon modulates neuroimmune responses following traumatic brain injury.bioRxiv : the preprint server for biology · 2026Article
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- Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study.Proteomics · 2025Article
- Guanine is an inhibitor of c-jun terminal kinases.Scientific reports · 2025Article
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- Deciphering Radiotherapy Resistance: A Proteomic Perspective.Proteomes · 2025Review
- Metabolomic liquid biopsy dynamics predict early-stage HCC and actionable candidates of human hepatocarcinogenesis.JHEP reports : innovation in hepatology · 2025Article
- Inflammatory disease progression shapes nanoparticle biomolecular corona-mediated immune activation profiles.Nature communications · 2025Article
- Application of Proteomic Methods in Oomycete Biology.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Sustained caloric restriction potentiates insulin action by activating prostacyclin synthase.Obesity (Silver Spring, Md.) · 2024Article
- Challenges of MS-based small extracellular vesicles proteomics.Journal of extracellular vesicles · 2024Review
- Microalgae and cyanobacteria as microbial substrate and their influence on the potential postbiotic capability of a bacterial probiotic.Microbial biotechnology · 2024Article
- Capture of RNA-binding proteins across mouse tissues using HARD-AP.Nature communications · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MS1-based label-free quantification can compare precursor ion peaks across runs, allowing reproducible protein measurements. Among bioinformatic platforms enabling MS1-based quantification, MaxQuant (MQ) is one of the most used, while Proteome Discoverer (PD) has recently introduced the Minora tool. Here, we present a comparative evaluation of six MS1-based quantification methods available in MQ and PD. Intensity (MQ and PD) and area (PD only) of the precursor ion peaks were measured and then subjected or not to normalization. The six methods were applied to data sets simulating various differential proteomics scenarios and covering a wide range of protein abundance ratios and amounts. PD outperformed MQ in terms of quantification yield, dynamic range, and reproducibility, although neither platform reached a fully satisfactory quality of measurements at low-abundance ranges. PD methods including normalization were the most accurate in estimating the abundance ratio between groups and the most sensitive when comparing groups with a narrow abundance ratio; on the contrary, MQ methods generally reached slightly higher specificity, accuracy, and precision values. Moreover, we found that applying an optimized log ratio-based threshold can maximize specificity, accuracy, and precision. Taken together, these results can help researchers choose the most appropriate MS1-based protein quantification strategy for their studies.
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