Isobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)

A vast assortment of human cell lines is available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, we determined the relative protein abundance profiles of a panel of eight diverse, but commonly studied, human cell lines. This panel includes: HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. We use a mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth. To this end, our strategy leverages TMTpro16-based sample multiplexing, high-Field Asymmetric Ion Mobility Spectrometry (FAIMS), and real-time database searching (RTS). The data show that cell line diversity was reflective of differences in the relative protein abundance profiles. We also determined that several hundred proteins were highly enriched for a given cell line and performed gene ontology and pathway analysis on these cell line-enriched proteins. We provide an R Shiny application to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection in addressing a given scientific inquiry or in improving an experimental design.