Top-Down Proteomics Analysis of pg-Level Cell Lysate Using Spray-Capillary CE-FAIMS-MS

However, CE-MS-based top-down proteomics of mass-limited samples remains challenging because of the need to handle ultralow sample amounts. Recently, we developed a spray-capillary CE-MS platform for ultrasensitive, low-volume top-down proteomics analysis, allowing for the detection of hundreds of intact proteoforms from pg-level samples.

Here, we integrated this platform with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to enhance proteoform coverage in mass-limited samples (i.e., samples with limited input mass). Our results suggested that FAIMS effectively enhanced the signal-to-noise ratio for pg-level samples by filtering background noise. At low injection masses (e.g., 1 pg), experiments performed with FAIMS yielded higher relative abundance than those conducted without FAIMS.