To investigate image quality as a function of number of projections and tube load per projection in compressive sensing (CS) based low-dose cone beam CT (CBCT), and achieve optimal low-dose scan protocols in image guided radiation therapy (IGRT). We have performed CS-based CBCT reconstruction with different combinations of number of projections (from 46 to 364) and mAs (from 0.2 to 2.4 mAs/view), which covers the whole clinically relevant range. Image quality is assessed in each case. On this basis, optimal scan protocols are analyzed according to various IGRT applications. Image quality degrades ∼10% when the imaging dose decreases from 400 to 100 total mAs, further ∼10% from 100 to 40 total mAs, and another ∼80% below 40 total mAs. Image quality on iso-low-dose lines at 36.8, 72.6, 109.2 and 145.6 total mAs varies 17.16%, 13.69%, 11.99% and 5.74% in terms RMSE with various scanning protocols. 1) In CS-based CBCT, image quality has little degradation with imaging dose> 100 total mAs. Optimal low-dose scan protocols likely fall in the range of 40-100 total mAs. 2) At a constant low-dose level, the scan protocol that with super sparse views (projection number < 50) is the most challenging case. 3) The optimal scan protocol is the combination of a medium number of projections and a medium level of mAs/view. This is more evident when the dose is ∼72.8 total mAs or below, and when the ROI is a low-contrast or high-resolution object. 4) The clinically acceptable lowest imaging dose level is task dependent. In our study, 72.8mAs is a safe dose level for visualizing low-contrast objects, while 12.2 total mAs is sufficient for detecting high-contrast objects of diameter greater than 3 mm. This work is supported in part by NIH (1R01CA154747-01), Varian Medical Systems through a Master Research Agreement, and the Thrasher Research Fund.