Fig. 2: Deep-scale proteome analysis of the micro-flow LC–MS/MS system.
From: Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS
a Summary of key experimental paramters and results comparing deep-scale proteome analysis data of HeLa and placenta protein digests using published nano-flow LC–MS/MS data and data obtained by micro-flow LC–MS/MS data in this study. b Box plots comparing Andromeda peptide identification scores of the data shown in a. Boxes and whiskers are defined as in Fig. 1b. The number of peaks used for each box are 303,597 (Kelstrup et al.31), 282,215 (Bache et al.29), 287,834 (This study, 200 µg HeLa), 304,278 (This study, 400 µg HeLa), and 276,306 (This study, Placenta). Boxes and whiskers are defined as in Fig. 1b. Source data are provided as a Source Data file for b. c Summary of the actual sample throughput that can be achieved by the micro-flow LC–MS/MS system presented in this study compared to a typical nano-flow LC–MS/MS setup. d Overlay of base peak chromatograms of the same high pH reversed phase chromatography fraction of a TMT11 labeled pepties from a deep-scale analysis of 11 human cancer cell lines analyzed by micro-flow (blue) and nano-flow (red) LC–MS/MS, each using a 15 min gradient. e Result summary for the deep-scale proteomic analysis of eleven TMT-multiplexed human cancer cell lines using nano-flow or micro-flow LC–MS/MS systems. f Density plot displaying the dynamic range of TMT quantification for common peptides from 11 human cancer cell lines obtained by measuring identical samples using the LC–MS/MS configurations as shown in e. Dynamic range of TMT quantification was defined as the ratio of the maximum and minimum intensity values of a peptide across the 11 TMT channels.
