Targeted protein quantification using sparse reference labeling

Targeted proteomics is a method of choice for accurate and high-throughput quantification of predefined sets of proteins. Many workflows use isotope-labeled reference peptides for every target protein, which is time consuming and costly. We report a statistical approach for quantifying full protein panels with a reduced set of reference peptides. This label-sparse approach achieves accurate quantification while reducing experimental cost and time. It is implemented in the software tool SparseQuant.