An SILAC quantification algorithm for LC-FTMS

Abstract

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.