Phosphoproteomic analysis of small cell populations is a challenge due to insufficient MS signal intensity, and the BASIL innovation of using isobaric labeling to ""boost"" a sample (e.g., a biological sample mimicking the study samples but available in a much larger quantity) in multiplexed analysis enables sensitive and comprehensive quantitative phosphoproteomic measurements with <100 000 cells. The BASIL strategy increases the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20 000 phosphorylation sites from human pancreatic islets treated with interleukin-1β and interferon-γ. Together, this signal boosting strategy provides an attractive solution for comprehensive and quantitative phosphoproteome profiling of relatively small populations of cells where traditional phosphoproteomic workflows lack sufficient sensitivity.