Intensity-based label-free proteomics using a quadrupole orbitrap mass spectrometer

We present a unique data set for benchmarking label free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Soluble Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences. The data set, which is available online, provides a unique opportunity to test the proteomic platform (instrumentation and software) in its ability to perform intensity based label free quantification. We show that the presented combination of informatics and instrumentation produces high precision and quantification accuracy.