Fig. 2

Single-cell data quality control and exploration. a The efficiency of delivering proteins from single cells is estimated as the distribution of ratios between reporter ions from single cells and 5-cell reference samples. Single-cell intensity shows 95% of the expected 1:5 ratio denoted by the red dotted line. The data were acquired by a Q-Exactive using pSCoPE with 100-cell isobaric carriers. b Distributions of reporter ion intensities from single melanoma, monocyte, and negative controls from the pSCoPE sets [27]. c MS1 intensity of precursors from single melanoma cells and from negative controls from the plexDIA sets [24]. d The protein content (estimated as the average reporter ion intensity) is plotted against the diameter of cells estimated from images. The correlation suggests consistent delivery of proteins. e Principal component analysis (PCA) of single cells acquired using pSCoPE with 100-cell isobaric carriers. The single cells cluster by cell type, melanoma, and U937 monocytes. Bulk samples of 200 cells labeled with TMTpro are also projected onto the PCA to evaluate the agreement between relative protein quantification in bulk and single-cell samples. A separate smaller cluster of melanoma cells is enclosed in a dotted circle. f Biological replicates of melanoma cells analyzed by pSCoPE or by plexDIA were jointly projected by PCA. The projections show alignment of two observed sub-clusters; the quantitative agreement is shown in Additional file 1: Fig. S12b