The spectral counts matrix has samples in the columns, and proteins in the rows. Each sample consists in 500ng of standard yeast lisate spiked with 100, 200, 400 and 600fm of a mix of 48 equimolar human proteins (UPS1, Sigma-Aldrich). The dataset contains a different number of technical replicates of each sample. This dataset has only 100 proteins of total 685 proteins in the original data for fast example execution. If you want to use whole dataset, go for 'example_data2'.
A data frame containing MS Run names and their corresponding experiment groups
Josep Gregori, Laura Villareal, Alex Sanchez, Jose Baselga, Josep Villanueva (2013). An Effect Size Filter Improves the Reproducibility in Spectral Counting-based Comparative Proteomics. Journal of Proteomics, DOI http://dx.doi.org/10.1016/j.jprot.2013.05.030