Extended Data Fig. 1 Graphic scheme of the trapping nano-LC system.

A large-i.d. trapping column (300 μm i.d.) and 65-cm-long, 75 μm i.d. C18 separation column, heated at 50 °C, are connected and operated by a six-port valve. The unique selective trapping-delivery strategy consists of three stages, including sample injection, cleanup and delivery. The red lines and arrows indicate the flow of the peptide sample in each stage.

Extended Data Fig. 2 Schematic illustration of the IonStar data processing workflow.

The IonStar data processing workflow encompasses the following components: first, generation of precisely defined UHR-MS1 quantitative features with an extremely narrow m / z window; second, accurate assignment of peptide IDs to the quantitative features after peptide/protein identification; third, a stringent post-feature-generation QC procedure to eliminate low-quality quantitative data at both feature and peptide level, followed by aggregation of the data to protein level; finally, a series of postprocessing data analysis tools for assessment of data quality, visualization of the quantitative results, statistical analysis and discovery of significantly changed proteins.

Extended Data Fig. 3 Quantitative precision and accuracy of proteins uniquely quantified by IonStar and of the lowest 25% abundance.

a , Intragroup CV (i.e., precision) of proteins that are uniquely quantified by IonStar that are of the lowest 25% in abundances. The numbers above the boxplots denote the number of proteins with the lowest 25% abundances that are uniquely quantified by IonStar. b , Relative quantitative errors of protein ratios (i.e., accuracy) of E. coli proteins with the lowest 25% abundance that uniquely quantified by IonStar. The number above the boxplots denotes the number of E. coli proteins uniquely quantified by IonStar and with the lowest 25% abundance.

Supplementary Information

Supplementary Methods, Figs. 1–4 and Tables 1–3

Reporting Summary