The attached file contains an excel document that consists of 2 worksheets.
Sheet 1 clarifies which Skyline library was used for each figure.
Sheet 2 is a legend for each Skyline file showing which replicate corresponds to a certain sample (e.g. which constructs were transfected, what cell line was used, used compound, which affinity sequence was used for pullout experiments, ...)
The skyline file "pfu_2016-01-21_09-10-33.sky.zip" present in the section "Targeted MS Runs" contains all results of the pyrococcus furiosus discovery runs.
The dat files resulting from the mascot searches are embedded as a spectral library, whereas the raw files are imported as result files. In this way all peptides can be visualized in the raw files together with the library match.