The debate still persists whether proteomics emerged from protein chemistry or is it a new field. Although proteomics employs the basic techniques and principles of protein chemistry its approach and ultimate goals are different. While protein chemistry has always dealt with single proteins, proteomics is more interested in studying the global proteome as a whole, making its usability for high-throughput studies. The approach of protein chemists has always been targeted: isolation of proteins followed by structural elucidation and functional analysis. On the other hand, proteomics has always taken up the challenge of studying large number of proteins together, and is more interested in the interactions between the proteins, which ultimately helps to understand the function of the protein. In a way, this approach leads to long-term goal of understanding the role of the protein in the cell or the organism. The protein chemists have emphasized on the structural aspects of the protein, while the proteomics researchers have aimed to look upon the proteins in terms of developing a mathematical model for the system as a whole, using a systems biology approach.

Protein chemistry began its sequence retrieval using Edman degradation technique, whereas proteomics does the same using mass spectrometry. Edman degradation method still holds good but only when there is limited number of proteins; however, for high throughput studies the mass spectrometry based sequencing has become the method of choice. The additional benefit of mass spectrometry based sequencing is that there is no need for sequencing the entire protein. Few peptide sequences and bioinformatic tools are sufficient to identify the protein. In summary, protein chemistry and proteomics have unique outlook of the problem, and methodology employed to address the problems; however, both are complimentary to each other.