ArticleJournal of proteome research2018
Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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
8 citing papers in PubMed.
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- MS1Connect: a mass spectrometry run similarity measure.Bioinformatics (Oxford, England) · 2023Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Improving Peptide-Level Mass Spectrometry Analysis via Double Competition.Journal of proteome research · 2022Article
- Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.Journal of proteome research · 2021Article
- mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection.Journal of proteome research · 2021Article
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments.Journal of proteome research · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high-resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine's scores are well calibrated, that is, that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum, has proven to be challenging. Here we describe a database search score function, the "residue evidence" (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a "combined p value" score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p value to the score functions used by several existing search engines. Our results suggest that the combined p value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit ( http://crux.ms ).
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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.