A comprehensive full factorial LC‐MS/MS proteomics benchmark data set

An important prerequisite for the development and benchmarking of novel analysis methods is a well‐designed comprehensive LC‐MS/MS data set. Here, we present our data set consisting of 59 LC‐MS/MS analyses of 50 protein samples extracted individually from Escherichia coli K12 and spiked with different concentrations of bovine carbonic anhydrase II and/or chicken ovalbumin, according to a 2 × 3 full factorial design. Using the well‐annotated and commonly used E. coli proteome as the sample background ensures that the complexity of the data is on a par with most current proteomic analyses. Data were acquired over a 2‐month period using multiple reversed‐phase columns and instrument calibrations to include real‐life challenges faced when analyzing large proteomics data sets. Moreover, so‐called “ground truth” data, comprised by LC‐MS/MS measurements of the pure spikes are included in the data set. The current manuscript elaborates this comprehensive benchmark data set for future development and evaluation of analysis methods and software.

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