Principal Component Analysis (PCA) of quantification results from SCoPE2 analysis

Evaluating protein quantification results from SCoPE2 analysis. (a) Distributions of relative reporter ion (RI) intensities for all samples from a single SCoPE2 set. The samples include carrier, reference, 5 single HeLa cells, 5 single U937 cells, a negative control well (Ctr −), and a positive control well (Ctr +) from diluted U937 cell lysate. Two of the TMT labels (between the reference and the single cells) are not used because they are affected by isotopic impurities of the TMT labels used for the carrier and the reference. The bin marked by > −3.5 corresponds mostly to RI intensities below the detection limit (missing values). (b) Distributions of coefficients of variation (CVs) for the relative quantification of proteins based on different peptides originating from the same protein. The CVs are computed both for the single cells and the negative control wells. (c) Principal component analysis (PCA) of 126 single cells and bulk samples. The PCA is based on 1756 proteins with about 1,000 proteins quantified per single cell. Panels b and c are generated by the SCoPE2 pipeline. For more details see: https://scope2.slavovlab.net/mass-spec/protocol