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. 2015 Apr 3;14(4):1979-86.
doi: 10.1021/pr501045t. Epub 2015 Mar 24.

MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer

Tali Shalit  1 , Dalia Elinger  1 , Alon Savidor  1 , Alexandra Gabashvili  1 , Yishai Levin  1
Affiliations

MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer

Tali Shalit et al. J Proteome Res. .

Abstract

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.

Keywords: informatics tools; label-free proteomics; quantification.

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