Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10229)


Estimating the false discovery rate (FDR) among a list of tandem mass spectrum identifications is mostly done through target-decoy competition (TDC). Here we offer two new methods that can use an arbitrarily small number of additional randomly drawn decoy databases to improve TDC. Specifically, “Partial Calibration” utilizes a new meta-scoring scheme that allows us to gradually benefit from the increase in the number of identifications calibration yields and “Averaged TDC” (a-TDC) reduces the liberal bias of TDC for small FDR values and its variability throughout. Combining a-TDC with “Progressive Calibration” (PC), which attempts to find the “right” number of decoys required for calibration we see substantial impact in real datasets: when analyzing the Plasmodium falciparum data it typically yields almost the entire 17% increase in discoveries that “full calibration” yields (at FDR level 0.05) using 60 times fewer decoys. Our methods are further validated using a novel realistic simulation scheme and importantly, they apply more generally to the problem of controlling the FDR among discoveries from searching an incomplete database.


Tandem mass spectrometry Spectrum identification False discovery rate Calibration 

Supplementary material

440120_1_En_7_MOESM1_ESM.pdf (2.1 mb)
Supplementary material 1 (pdf 2118 KB)


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.School of Mathematics and Statistics F07University of SydneySydneyAustralia
  2. 2.Department of Genome Sciences, Department of Computer Science and EngineeringUniversity of WashingtonSeattleUSA

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