The 4800 MALDI TOF/TOF Analyzer, for protein biomarker discover, combines the Applied Biosystems/MDS SCIEX TOF/TOF optics technology with the OptiBeam on-axis laser, which increases the number of ions directed into the ion path to increase sensitivity. QuanTIS precursor ion allows specific isolation of precursor ions designated for MS/MS, thus achieving accurate and easy-to-interpret results. Proprietary iTRAQ and ICAT reagents further enable biomarker discovery by permitting relative and absolute protein quantitation. The increased sensitivity and expanded dynamic range of the analyzer yields high-confidence protein identifications, enables multiplex studies with the use of the iTRAQ reagents, and enables true results-dependent analysis with or without tagging chemistry, such as ICAT reagents. GPS Explorer Software supports automated, intelligent analysis of complex samples by focusing on collecting clean data with high relevance. Opti-TOF disposable, large format sample plates maximize throughput, minimize sample carry over, and make sample handling and archiving convenient.