Fig. 3: Comparison of identification coverage and quantitation performance of proteomic profiling of PC-9 cells by DIA and DDA methods. | Nature Communications

Fig. 3: Comparison of identification coverage and quantitation performance of proteomic profiling of PC-9 cells by DIA and DDA methods.

From: Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

Fig. 3: Comparison of identification coverage and quantitation performance of proteomic profiling of PC-9 cells by DIA and DDA methods.

a Comparison of protein groups and peptides identified by triplicate analysis using the data-dependent acquisition (DDA, light blue) and data-independent acquisition (DIA, light green) modes. Single-shot DIA was acquired and processed by both library-based DIA (libDIA) and direct DIA (dirDIA) approaches by Spectronaut. b Overlap of protein groups identified by DDA and DIA. c Distribution of coefficient of variation (CV%) for quantified protein groups by DDA and DIA. d Evaluation of missing values (%) of proteins identified and quantified in triplicate LC–MS/MS runs by DDA and DIA. e Assessment of dynamic range based on protein abundance rank and annotation of selected proteins related to lung cancer. Source data are provided as a Source data file.

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