Proteomics refers to a group of analytical techniques for high throughput protein analysis, providing evidence for protein expression levels, subcellular localization, post-translational modifications and molecular interactions. As such, proteomics has contributed largely to our knowledge regarding molecular mechanisms underlying health and disease and pinpointed potential disease biomarkers. The scope of this review is to briefly introduce the principles of major proteomics techniques employed in biological research, including novel quantitative and molecular imaging mass spectrometry-based platforms. A few examples from the application of these techniques in biomarker discovery for kidney diseases are also provided.