We have studied proteins and proteomes for decades using diverse methods. Yet, our studies and methods have been rather limited to hypothesis testing. As a result, the proteome remains a frontier that awaits to be investigated with unbiased discovery-driven methods that can reveal its secrets.

The most common methods for studying proteomes are focused on hypothesis testing and are thus challenged to make discoveries that have not yet been hypothesized. Edman sequencing and mass spectrometry can de novo sequence proteins, but such sequencing has been too slow and expensive to be practically applied to even a single proteome. The emerging single molecule methods have not demonstrated de novo sequencing, even when commercials indicate otherwise. As a result, large scale protein analysis is based on hypothesis testing. These hypotheses usually originate from nucleic acid analysis and are tested by the detection of epitopes (usually with limited specificity) or fingerprinting of peptides and proteins. Thus, aspects of the proteome that are not easily detected by nucleic acid sequencing are unlikely to be tested and discovered. As a result, the tested hypotheses are biased by investigator choices and/or the abundance of the associated protein products.

These are sobering limitations.

The limitations have hampered hypothesis-free discovery and exploration of proteomes. Yet, these limitations are not based on physical laws. They reflect technological challenges, societal priorities shaping funding allocation, and insufficient scientific creativity to transcend the challenges. These are major obstacles, and yet they are all surmountable. Even better, the remarkable progress underway is encouraging evidence that we may soon break the shackles of hypothesis testing. We may soon enter an age of discovery when proteomes are routinely explored at scale and their secrets revealed.