Mass spectrometry has become the main technique in proteomics study. And the strategy has been recently changed to focus more on research of target proteins from comprehensive proteins, because characterization of target proteins and quantitative study of protein biomarkers could provide important knowledge for drug discovery and development. Protein biomarkers and PTM (post-translational modification) are the main targets in target protein research called focused proteomics. However, biomarker

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... discovery and PTM research are challenging due to difficulty in detection. A phosphate group of a compound could decrease ionization efficiency, which makes the detection of phosphorylated proteins more difficult. Most biomarkers are low abundant proteins, so detection of such compounds from highly complex samples like serum and cell lysate is not easy without sample fractionation using multi dimensional LC. The difficulty of proteomics technology using mass spectrometry results from lack of a tool to detect target proteins directly in complex samples. Here we introduce a strategy to detect a target protein directly even in a low concentration sample (e.g., PTM sample and low abundant biomarker) without additional fractionation. In this strategy unique scan modes of 4000 Q TRAP ® system, precursor ion scan and MRM are key features to remove contaminant signal in chromatogram. We also show successful examples of the detection of phosphorylated peptides from digested protein kinase, the verification of low abundant protein using a new tool, "MIDAS TM workflow", and the monitoring for variation of phosphorylation sites using iTRAQ TM reagent.