ArticleJournal of proteome research2015
On the importance of well-calibrated scores for identifying shotgun proteomics spectra.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- A learned score function improves the power of mass spectrometry database search.Bioinformatics (Oxford, England) · 2024Article
- Observations from the Proteomics Bench.Proteomes · 2024Article
- Improving Peptide-Level Mass Spectrometry Analysis via Double Competition.Journal of proteome research · 2022Article
- High-confidence structural annotation of metabolites absent from spectral libraries.Nature biotechnology · 2022Article
- Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.Journal of proteome research · 2021Article
- New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics.Bioinformatics (Oxford, England) · 2020Article
- ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching.Journal of proteome research · 2018Article
- Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data.Journal of proteome research · 2018Article
- Controlling the FDR in imperfect matches to an incomplete database.Journal of the American Statistical Association · 2018Article
- Gradients of Generative Models for Improved Discriminative Analysis of Tandem Mass Spectra.Advances in neural information processing systems · 2017Article
- Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2017Article
- Article
- Tandem Mass Spectrum Identification via Cascaded Search.Journal of proteome research · 2015Article
- Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.Journal of proteome research · 2015Article
- Mass spectrometrists should search only for peptides they care about.Nature methods · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Identifying the peptide responsible for generating an observed fragmentation spectrum requires scoring a collection of candidate peptides and then identifying the peptide that achieves the highest score. However, analysis of a large collection of such spectra requires that the score assigned to one spectrum be well-calibrated with respect to the scores assigned to other spectra. In this work, we define the notion of calibration in the context of shotgun proteomics spectrum identification, and we introduce a simple, albeit computationally intensive, technique to calibrate an arbitrary score function. We demonstrate that this calibration procedure yields an increased number of identified spectra at a fixed false discovery rate (FDR) threshold. We also show that proper calibration of scores has a surprising effect on a previously described FDR estimation procedure, making the procedure less conservative. Finally, we provide empirical results suggesting that even partial calibration, which is much less computationally demanding, can yield significant increases in spectrum identification. Overall, we argue that accurate shotgun proteomics analysis requires careful attention to score calibration.
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