The transcription system of archaea has both bacterial-like and eukaryotic-like features. Only a very limited number of archaeal transcription regulatory proteins have been identified to date, and transcription regulatory pathways are far from being well known. The primary goal of this study is to take advantage of the bioanalytical approaches and targeted proteomics strategy to discover and characterize new transcription factors in Pyrococcus furiosus (Pf), a model archaeal organism. It describes how a new transcription factor was discovered by using DNA-affinity protein purification, mass spectrometry identification and further protein characterization methods. The book is a good example for new biological discovery led by integration of multiple scientific strategies, including molecular biology, bioanalytical chemistry and bioinformatics. It will be useful to students and researchers who are interested in DNA-binding proteins, mass spectrometry methods, computation directed biological study and Archaeal biology.