Single Cell Proteomics and the Carrier Proteome Effect

Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method that utilizes isobaric labels to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the technologies underlying SCoPE-MS - isobaric labels and mass spectrometry - comprise technical limitations with the potential to unfavorably impact data quality and biological interpretation. These limitations are due to the carrier proteome, a sample added at 25-500x single cell proteomes to enable peptide identifications. Here, we perform SCoPE-MS experiments with increasing amounts of carrier proteome and evaluate quantitative accuracy as it relates to mass analyzer dynamic range, multiplexing level, and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy – we term this the carrier proteome effect. Based on our findings, we provide guidance on experimental design, data collection, and data analysis to limit the impact of the carrier proteome effect within SCoPE-MS measurements.