Multiple competition-based FDR control and its application to peptide detection

DOI10.1007/978-3-030-45257-5_4MaRDI QIDQ5041797zbMATH OpenOpenAlexFDO

Authors Kristen Emery, Syamand Hasam, Uri Keich, William Noble

Publication date 14 October 2022

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1907.01458

zbMATH Keywords

false discovery ratemultiple hypothesis testingpeptide detectiontandem mass spectrometry

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Abstract: Competition-based FDR control has been commonly used for over a decade in the computational mass spectrometry community (Elias and Gygi, 2007). Recently, the approach has gained significant popularity in other fields after Barber and Candes (2015) laid its theoretical foundation in a more general setting that included the feature selection problem. In both cases, the competition is based on a head-to-head comparison between an observed score and a corresponding decoy / knockoff. Keich and Noble (2017b) recently demonstrated some advantages of using multiple rather than a single decoy when addressing the problem of assigning peptide sequences to observed mass spectra. In this work, we consider a related problem -- detecting peptides based on a collection of mass spectra -- and we develop a new framework for competition-based FDR control using multiple null scores. Within this framework, we offer several methods, all of which are based on a novel procedure that rigorously controls the FDR in the finite sample setting. Using real data to study the peptide detection problem we show that, relative to existing single-decoy methods, our approach can increase the number of discovered peptides by up to 50% at small FDR thresholds.

Recommendations

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• scientific article; zbMATH DE number 720689

Cites work

• A Direct Approach to False Discovery Rates
• Controlling the false discovery rate via knockoffs
• Controlling the FDR in imperfect matches to an incomplete database
• scientific article; zbMATH DE number 720689 (Why is no real title available?)
• IPAD: stable interpretable forecasting with knockoffs inference
• Significance analysis of microarrays applied to the ionizing radiation response
• Statistical significance for genomewide studies
• Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach

Cited in

(5)

• Null-free false discovery rate control using decoy permutations
• Controlling the FDR in imperfect matches to an incomplete database
• CONTROLLING THE FALSE DISCOVERY RATE THROUGH MULTIPLE COMPETITION
• Local false discovery rate estimation with competition-based procedures for variable selection
• Competition-based control of the false discovery proportion

Describes a project that uses

Uses Software

• qvalue
• DeepPINK
• GitHub

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