When it comes to proteomics and broad protein profiling (and/or quantification), two main technologies come to mind: Mass Spectrometry and Antibody Arrays. Rather than opposing each other, they appear more as complementary in the chase for Biomarker discovery.
Indeed, each technique has its own advantages and limitations. Combining the two can contribute to more accurate identification of relevant biomarkers. Going one step further, biomarker identification performed by Mass Spec can be confirmed by Antibody Arrays.