MS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer

Presented is a data set for benchmarking
MS1-based label-free quantitative
proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest
in four different concentrations, simulating protein expression differences
in a background of an unchanged complex proteome. The data set provides
a unique opportunity to evaluate the proteomic platform (instrumentation
and software) in its ability to perform MS1-intensity-based label-free
quantification. We show that the presented combination of informatics
and instrumentation produces high precision and quantification accuracy.
The data were also used to compare different quantitative protein
inference methods such as iBAQ and Hi-N. The data
can also be used as a resource for development and optimization of
proteomics informatics tools, thus the raw data have been deposited
to ProteomeXchange with identifier PXD001385.