title: MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer.
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.
authors.affiliation: †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Tali
authors.initials: T
authors.lastname: Shalit
authors.affiliation: †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Dalia
authors.initials: D
authors.lastname: Elinger
authors.affiliation: †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Alon
authors.initials: A
authors.lastname: Savidor
authors.affiliation: †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Gabashvili
authors.affiliation: †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Yishai
authors.initials: Y
authors.lastname: Levin
mesh_terms: D019985:Benchmarking / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli; D005786:Gene Expression Regulation / Q000502:physiology*; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods*; D040901:Proteomics / Q000379:methods*
keywords: informatics tools; label-free proteomics; quantification