These findings demonstrate that the incorporation of predicted features from MS 2 PIP and DeepLC with MS 2 Rescore enhances the number of identifications at a 1% FDR threshold for single-cell proteomics data. The data sets were acquired with an injection time of 500 ms and 750 ms, respectively. The number of confidently identified spectra for all files in each of the data sets by MS Amanda (orange), MS Amanda with Percolator (green) and MS Amanda in combination with MS 2 Rescore (blue).