ArticleJournal of proteome research2021
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection.
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, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 70 citations in OpenAlex.
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Cigarette smoke induces FASN-dependent fatty acid metabolic rewiring to drive bladder cancer progression.Cancer letters · 2026Article
- Instrument-Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring Methods.Journal of proteome research · 2026Article
- Unfolded Protein Response as a Therapeutic Target: 4-(Heptyloxy)phenol Induces Programmed Cell Death in Ewing Sarcoma.Molecular cancer therapeutics · 2026Article
- Foundation model enables interpretable open and error-tolerant searching for mass spectrometry-based proteomics.Bioinformatics (Oxford, England) · 2026Article
- DDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics.Nature communications · 2026Article
- Mass spectrometry imaging tutorial: From cancer biomarker discovery to clinical applications.Analytica chimica acta · 2026Review
- Regulation of BCL11A DNA binding and expression in human erythrocyte precursor HUDEP-2 cells.bioRxiv : the preprint server for biology · 2026Article
- High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MSMethods in molecular biology (Clifton, N.J.) · 2026Article
- A distinct PP2A subunit regulates local protein phosphorylation at the axon initial segment.Nature communications · 2025Article
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing.Journal of proteome research · 2025Article
- A haplotype-resolved view of human gene regulation.bioRxiv : the preprint server for biology · 2025Article
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.Journal of proteome research · 2025Article
- Unifying the analysis of bottom-up proteomics data with CHIMERYS.Nature methods · 2025Article
- Tobacco smoke exposure is a driver of altered oxidative stress response and immunity in head and neck cancer.Journal of translational medicine · 2025Article
- Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.Journal of proteome research · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Proteomics studies rely on the accurate assignment of peptides to the acquired tandem mass spectra-a task where machine learning algorithms have proven invaluable. We describe mokapot, which provides a flexible semisupervised learning algorithm that allows for highly customized analyses. We demonstrate some of the unique features of mokapot by improving the detection of RNA-cross-linked peptides from an analysis of RNA-binding proteins and increasing the consistency of peptide detection in a single-cell proteomics study.
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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.