Map of Acquisition set up. Pool 1 represented a master pool of a single digest of pooled plasma, injected in 7 replicates for monitoring MS-QC performance. There were an additional 10 pools (Pool 7, Pool, 7, Pool 11, ... etc) comprised of separate aliquots of a master QC pool, each digested separately for monitoring sample preparation as well as MS QC. Samples from CAD and Control patients were randomized throughout the acquisition (blue and red dots & bars) 

Figure 5. (A) Boxplots representing the distribution of abundance for the 10 proteins selected by the elastic net function as the most parsimonious set of classifiers for a logistic regression analysis predicting CAD status. Each individual measurement is shown as a filled circle overlaid on the box plot for that group. (B) Boxplots showing the distribution of the model-derived probability of CAD plotted for the true control and true CAD groups. (C) Bar graphs demonstrating the individual protein intensity values for each of the model selected proteins as measured for each of 10 different patients, five with the highest model predicted probability of CAD and five with the lowest model predicted probability of CAD. (D) Receiver operating characteristic (ROC) curve plotting the sensitivity and specificity of the CAD-prediction model. 

Raw data used to generate the spectral library upon which the DIA-MS files were searched, and the MRM experiment was designed, are uploaded here, in the "LibraryData" folder, and their Spectrast file and the final library can be found on a previously shared public site:  http://www.peptideatlas.org/PASS/PASS01066 from their publication in the Circulation 2018 paper "Proteomic Architecture of Human Coronary and Aortic Atherosclerosis" which can be viewed here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6011234/