2026-10-13T00:20:23Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33839015 2026-09-16T10:05:31Z category_1 category_4 category_146 category_16 category_21 category_272 category_873 category_39 category_734 category_69 portal_63 item_type_3 month_year_09_2026

Top-Down Proteomics Analysis of pg-Level Cell Lysate Using Spray-Capillary CE-FAIMS-MS Samin Anjum (18529890) Zhitao Zhao (4956574) Kellye A. Cupp-Sutton (8138136) Si Wu (154794) Biophysics Biochemistry Space Science Physiology Biotechnology Environmental Sciences not elsewhere classified Chemical Sciences not elsewhere classified Ecology Biological Sciences not elsewhere classified Inorganic Chemistry traditional liquid chromatography intensity commonly reported enhance proteoform coverage filtering background noise low injection masses analyzing intact proteoforms limited biological samples implemented 2d ce faims effectively enhanced conducted without faims e ., samples ms capillary electrophoresis intact proteoforms limited samples noise ratio level samples capillary ce substantial loss sensitivity compared results suggested promising technique holds potential Capillary electrophoresis-mass spectrometry (CE-MS) is a promising technique for ultrasensitive top-down proteomics due to its high resolution and sensitivity compared with traditional liquid chromatography (LC)-based methods. 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. Interestingly, in all cases, we did not observe the substantial loss in intensity commonly reported for bottom-up proteomics with FAIMS. Additionally, we implemented 2D CE-FAIMS-MS by applying five different FAIMS compensation voltages (CVs) for gas-phase intact proteoform fractionation. This platform detected >3000 yeast proteoforms using 100 pg per CV. Overall, our results suggested that the spray-capillary CE-FAIMS-MS platform enables deep proteoform characterization of pg-level samples and holds potential for analyzing intact proteoforms in mass-limited biological samples. 2026-09-16T00:00:00Z Dataset Dataset 10.1021/acs.jproteome.6c00353.s002 https://figshare.com/articles/dataset/Top-Down_Proteomics_Analysis_of_pg-Level_Cell_Lysate_Using_Spray-Capillary_CE-FAIMS-MS/33839015 CC BY-NC 4.0