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.
While Antibody arrays can allow profiling of up to 2000 human proteins (see my previous post on the recently released L2000 array for more details), MS capacity in terms of number of proteins is higher and does not require protein specific tools like antibodies do. However, abundant proteins can be an issue in Mass Spec, while removal of these abundant proteins is not necessary when working with Antibody Arrays. Antibody arrays are spotted in such way to allow single sample dilutions for proteins of very broad expression ranges in a single experiment. This is where the two technologies can really complement each other.
Another advantage of antibody array is evidently the cost of the equipment. Whether for Chemiluminescent detection or fluorescent detection, the equipment required is quite standard nowadays whereas MS equipment can be quite costly. If you’d like to know more about this, there is an interesting recent post written by Raybiotech Scientists that should be of interest to you.