Leveraging automated sample prep enabled by Tecan Fluent integrated with on-deck plate based sonicator (Covaris R230) for lysis, bead washing, and rapid digestion, sample prep is parallelized with 48 samples/day DIA acquisition (Thermo Astral).
Tandem Vanquish Neo enables simultaneous equilibration/loading of a second 75um/40cm nano LC column while LC-MS acquisition occurs on the first, unlocking 48 samples/day acquisition at nanoflow rates without sacrificing chromatography or gradient length
Quantitative comparison of the six cell lines reveals well-defined signatures of protein abundance across more than 13,000 protein groups with protein abundance measurement variability (within cell line) less than 10% CV. Within a given cell line (example: HCT116) protein abundance measurements span > 3X10^6 fold intensity. We observe excellent data completeness across experimental replicates of the same sample type (example: HCT116) where 10927/12833 (85%) of all proteins are detected in 16/16 replicates.
Analysis of individual proteins reveals precise measurements of both large and subtle expression level changes distinguishing between cell lines with excellent agreement across replicates and the ability identify proteins that are truly absent in certain sample types. Confident interpretation of cell line differentiation factors combined with high-throughput sample preparation and analysis are ideally suited for biomarker discovery or off-target profiling