A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

By Mikhail M. Savitski, Mathias Wilhelm, Hannes Hahne, B. Kuster, Marcus Bantscheff. Molecular & Cellular Proteomics, 2015

391 citations recorded by the source corpus.

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target–decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target–decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The “picked” protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The “picked” target–decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used “classic” protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/3b3384926168e7af70d71e65073088024e28278f

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Citations in the corpus

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0 (2016, methodology): “Overall, we concluded, in agreement with Savitski et al. [10], that the best-scoring peptide approach yielded the best overall performance.”
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (2019, methodology): “, 2003) were filtered to 1% protein-level False Discovery Rate (FDR) using the chosen FDR target-decoy strategy and the best peptide approach (allowing both unique and razor peptides) and applying the picked FDR strategy (Savitski et al., 2015).”
Quantitative Proteomics of the Cancer Cell Line Encyclopedia (2020, positive): “Using the Picked FDR method (Savitski et al., 2015) proteins were filtered to the target 1% level.”