It is worth noting that the total number of identifications, when using Percolator, which exclusively relies on features directly extracted from the MS Amanda output file, and MS 2 Rescore, which additionally incorporates predicted features, does not differ as significantly as has been observed for other data set types. One potential explanation for this observation may be the lower performance of the MS 2 PIP models, which have been trained using bulk proteomics experiments rather than single-cell data. Due to the notably low protein abundance in single-cell experiments, the fragment ions in the MS2 spectra may exhibit divergent fragmentation patterns and intensity patterns compared to MS2 spectra from bulk experiments. Indeed, Boekweg and colleagues have shown that MS2 spectra from single-cell proteomics experiments showcase altered fragmentation spectra. In general, fewer peaks are observed, and these peaks exhibit reduced intensity, making the differentiation between signal and noise more challenging in spectra from single-cell experiments.