Extended Data Fig. 3: Characterization of HeLa/K562 carrier level dilutions and public SCP data.

a, The measured carrier proteome ratio vs. the number of ions (sum s/n) for each quantified spectrum (scatter plot). All spectrum from (a) were ordered by descending number of ions (sum s/n) and the top 50% of the data (highest s/n) was used to create a distribution of carrier proteome ratios (density plot). The carrier proteome ratios were derived from the median of the distribution. b, Analysis of quantitative data relating to peptide identifications for data from Duo et al. (NanoPots) and Specht et al. (SCoPE-MS). Signal-to-noise—Density plot of the summed s/n for all reporter ions extracted from peptide spectral matches (PSMs) in external single cell proteomics experiments. Ion flux (s/n per ms) – Density plot of the ion flux as extracted from PSMs in external single cell proteomics experiments. ‘Ion flux’ represents the number of ions (s/n) measured per millisecond (ms) of injection time. This measurement provides a readout on the complexity of the sample and the sensitivity of the mass spectrometer. c, For each identification, the CV within cell type was calculated and the number of ‘single cell’ ions (quant s/n) within all reporter channels was recorded. Measurements were grouped into bins of 20 quant s/n and the median CV of each bin was plotted as a function of the number of ions. Data were separated by cell type. d, Same analysis as (c), but omitting channel 127n from the analysis.