ArticleJournal of the American Society for Mass Spectrometry2016
Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0.
Article in Journal of the American Society for Mass Spectrometry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 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
236 citing papers in PubMed.
- Article
- Interactions of LINE-1 ORF1p with proteins and chromatin suggest a role in neuronal physiology.Life science alliance · 2026Article
- Automated prototyping of genetic codes.Nature · 2026Article
- Article
- Identification of Gβ5 Interactome Associated with Neuronal Development in Neuro-2a Cells through miniTurbo Proximity Labeling.ACS omega · 2026Article
- CReP-mediated control of eIF2α phosphorylation is a critical node in MYC-driven medulloblastoma.Nature communications · 2026Article
- Photosensitizer proximity labeling captures the lipid and protein interactomes.Nature chemical biology · 2026Article
- PolyQ-expanded ataxin-3 is associated with mitochondrial alterations in Machado-Joseph disease.Disease models & mechanisms · 2026Article
- Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation.The Journal of biological chemistry · 2026Article
- MSstatsQC-ML: A Supervised Machine Learning Approach to Monitor System Suitability and Quality Control in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Article
- Improved Protein Identification in Shotgun Proteomics with a Group-Level Extension of the LPGF Model.Journal of proteome research · 2026Article
- Fractionated proteomics identifies a protein network mitigating resistance exercise-induced damage in human skeletal muscle.Nature communications · 2026Article
- Proteogenomic analysis of the differential stability of cardiac protein isoforms.bioRxiv : the preprint server for biology · 2026Article
- Human 28S rRNA analysed by state-of-the-art oligonucleotide mass spectrometry: benchmarking current capabilities and a call to action for MS-Seq.bioRxiv : the preprint server for biology · 2026Article
- CD133 Shapes Extracellular Vesicle Cargo and Angiogenic Function in Basal-Like Triple-Negative Breast Cancer.Journal of extracellular vesicles · 2026Article
- Targeted enzymatic therapy for coeliac disease.EMBO molecular medicine · 2026Article
- In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.Molecular & cellular proteomics : MCP · 2026Article
- Improved Peptide Search for Identification of SUMO and Sequence-Based Modifiers, in MaxSBM.Molecular & cellular proteomics : MCP · 2026Article
- Soma-to-germline miRNA inheritance through yolk promotes stress resilience in progeny.Nature structural & molecular biology · 2026Article
- A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.Cell reports. Medicine · 2026Article
176 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.
Funding
Abstract
Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method-grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein-in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license. Graphical Abstract ᅟ.
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.