Table 2.

Summary of the main computational tools developed in single-cell proteomics.

Software Name	Software Info
Ion current extraction Re-quantification (IceR)	High rates of data-dependent acquisition identification with low missing value rates. More reliably quantified proteins and improved discriminability between single-cell populations.
Peptide identification algorithms (SEQUEST)	Normalize the theoretical spectra by forcing the b-type and y-type ions to be the most intense. It calculates the correlation score (Xcorr) and the ΔCn score.
Data-driven Alignment of Retention Times for IDentification (DART-ID)	Leverage reproducible retention times to increase peptide identifications in LC-MS/MS proteomics. Useful for MS2-based quantification.
Data-driven Optimization of MS (DO-MS)	Diagnose LC-MS/MS problems and enable to rationally optimize them. Data are visualized as full distributions using vertically oriented histograms, allowing subpopulations of ions to be identified.