Recent technological progress in ultrasensitive mass spectrometry and related analytical areas, have increased the analytical depth of proteomics such that single cell analysis is now possible. Such assays were previously reserved to genomics techniques with nucleic acid sequence amplification. In contrast to genomics techniques, analyzing protein function we are focused on direct elements executing biological program which later is reflected in cell/tissue phenotype.
Ultrasensitive mass spectrometry is superior in providing absolute amount and quantification of protein, metabolites in the single cell giving the information depth any of genomics approaches cannot provide.
Using Bruker timsTOF-SCP platform with in house manufactured tools, we have developed the pipeline which allows to study on the single level effect of pharmacological perturbation. Optimized single cell isolation strategy and handling allowed us to avoid losses which further is reflected in isolation and protein extraction consistency as a prerequisite of reliable measurement.
Our strategy allows us cross check single cell performance against multiplied cell isolations. Such quality check further ensures data quality and reliability.
Along the experimental pipeline for single cell analysis, we have developed computational approach to assess the quality. It helps data interpretation and integration tackling different parameters of the analysis.
Taken together, our approach opens new areas in single cell biology on the phenotype level not seen before.