Figure 1.

Conceptual comparison of data analysis performed by current tools versus HyperQuant. Current tools cannot quantitate the HOM data correctly. Manipulating label definitions in search tools (SILAC-Light, SILAC-Medium, and SILAC-Heavy) can help in the identification of PSMs but not correct protein quantitation whether MS¹-based search (SILAC search) or MS²-based search (iTRAQ/TMT) is used. (A) MS¹ quantitative search will combine the quantitative contribution from all six time points of each SILAC into the respective MS¹ peaks (L/M/H), as depicted by the colored boxes (light blue, light red, and light yellow). (B) MS² search only allows identification and quantitation of SILAC light-based reporters. The SILAC medium and SILAC heavy reporters will not be identified or quantified. (C) HyperQuant combines data from A with reporter quantitation from QuantWiz^IQ to correctly carry out quantitation across each SILAC-iTRAQ combination separately.