For large sample cohorts, our automated data-independent acquisition (DIA) workflow characterizes proteome-wide changes in protein expression with high depth and throughput.
At a glance
- More than 10,000 proteins and 200,000 peptides identified per sample
- Automated sample preparation on a Tecan Fluent liquid handler
- Tandem Vanquish Neo nanoLC coupled to an Orbitrap Astral: 48 samples per day
- Suited to degrader profiling, biomarker discovery and large cohort studies, in cell lines, tissues and biofluids
How it works
Sample preparation runs on a Tecan Fluent with an on-deck Covaris plate sonicator for lysis, followed by automated bead washing and rapid digestion, so preparation keeps pace with acquisition. A tandem Vanquish Neo setup equilibrates and loads a second 75 µm × 40 cm nanoLC column while the first is acquiring. That delivers 48 samples per day at nanoflow rates without shortening the gradient, with about 90% instrument utilization.
Example data: six cell lines, 16 replicates each
Six cell lines were each analyzed in 16 replicates, 96 samples in all. The study identified 13,393 protein groups and 244,727 unique peptides, with clear cell-line-specific signatures and a median within-cell-line coefficient of variation below 10%. In HCT116 cells, protein abundances span more than 3 × 10⁶-fold, and 10,927 of 12,833 proteins (85%) were detected in all 16 replicates.
Spotlight: individual proteins
FOLR1, RASF2 and B3A2 show precise, cell-line-specific profiles with close agreement across replicates, including proteins that are truly absent in some cell lines. That combination of depth and throughput suits biomarker discovery and off-target profiling.
