The sample data in this project is from the sample data published with the following paper:

Jacob D. Jaffe, D. R. Mani, Kyriacos C. Leptos, George M. Church, Michael A. Gillette, and Steven A. Carr, "PEPPeR, a Platform for Experimental Proteomic Pattern Recognition", Molecular and Cellular Proteomics; 5: 1927 - 1941, October 2006

The data itself consists of 50 mzXML files described in the paper as the "Variability Mix" and downloaded from the Tranche service of the Proteome Commons at the following address:

The data sets are derived from two sample protein mixes, alpha and beta, with varied concentrations of a specific list of 12 proteins. The samples were run on a Thermo Fisher Scientific LTQ FT Ultra Hybrid mass spectrometer. The resulting datafiles were converted to the mzXML format that was downloaded from Tranche.

We are indebted to the PePPER team at the Broad Institute for this sample data, as it is very useful for demonstrating and comparing multiple approaches to label-free quantitation.

NOTE: An earlier version of this page described the mix as "spiked into a background of mitochondrial mouse proteins". The Broad Institute informed me that the mzXML files posted on Tranche were mixes of the 12 proteins only.