ArticleJournal of proteome research2014
Fast and accurate database searches with MS-GF+Percolator.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 2 of them syntheses that pooled it.
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
59 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Comprehensive proteomics and meta-analysis of COVID-19 host response.Nature communications · 2023Pooled it
- Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.FEMS microbiology ecology · 2016Guideline
- BioProEV: A Bioinformatics Pipeline for Biologically-Relevant Handling of Missing Values in the Analysis of Extracellular Vesicles by Mass Spectrometry.Journal of extracellular biology · 2026Article
- Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics.Communications chemistry · 2025Article
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- The DNA methylation landscape of primary triple-negative breast cancer.Nature communications · 2025Article
- Functional-proteomics-based investigation of the cellular response to farnesyltransferase inhibition in lung cancer.iScience · 2025Article
- Plant stress and proteomics in medicinal plants.Frontiers in plant science · 2025Review
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- Delineating functional and molecular impact of ex vivo sample handling in precision medicine.NPJ precision oncology · 2024Article
- Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.iScience · 2024Article
- Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells.Journal of experimental botany · 2023Article
- Deep thermal profiling for detection of functional proteoform groups.Nature chemical biology · 2023Article
- Proteomic analysis reveals microvesicles containing NAMPT as mediators of radioresistance in glioma.Life science alliance · 2023Article
- Article
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.Briefings in bioinformatics · 2023Article
- MSMolecular & cellular proteomics : MCP · 2022Article
- SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry.Nature protocols · 2022Review
- Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome.Cancer research communications · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.
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.