An SILAC quantification algorithm for LC-FTMS

Stable isotope labeling by amino acids in cell culture (SILAC) [1] plays an important role in protein biomarker discovery based on liquid chromatography-mass spectrometry (LC-MS). Improvement in quantification accuracy in SILAC labeled LC-MS is needed for reliable biomarker discovery which has been plagued by high false-positive rates. In this paper, we consider various factors, such as interference, noise, and instrument suppression, that influence quantification accuracy, based on which we propose an algorithm with improved performance. Testing on samples with predefined heavy-to-light ratios, shows that our algorithm outperforms leading software by a significant margin in both measures of accuracy and precision.