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Mokapot improves the detection of RNA-cross-linked peptides from open modification search results. The nonlinear XGBoost classifier resulted in the detection of more modified (a) PSMs, (b) peptides, and (c) proteins over a linear SVM (the default model in mokapot) or the MSFragger E-value. (d) The XGBoost classifier gained PSMs over the linear SVM with mass shifts that correspond to known modifications at 1% FDR (q-value ≤0.01).
