CITE-Seq is a sequencing-based technique that combines single-cell RNA sequencing with cell surface protein analysis, offering a comprehensive view of both transcriptomes and proteomes within individual cells. Although this technique offers several advantages, it does come with a few limitations too. 

• By simultaneously analyzing RNA and protein levels, CITE-seq provides a more complete understanding of cellular functions at single-cell level. 
• Merging both measurements by directly linking the RNA profile of a cell with tis cell-surface protein expression allows researchers to address the discrepancy wherein only a fraction of the cells in a cell population have abundant surface proteins.  
• The use of barcoded antibodies allows researchers to analyze a near-limitless number of cell markers, making CITE-seq highly scalable and suitable for high-throughput studies.
• CITE-seq is especially valuable in pharmaceutical applications, particularly drug development, as a large number of cell-surface proteins serve as key diagnostic biomarkers or therapeutic targets.