An observation operator in data assimilation was formalized based on the signatures extracted from the integral quantities contained within observed vertical profiles in the ocean. A four-dimensional variational global ocean data assimilation system, founded on this observation operator, was developed and utilized to conduct preliminary data assimilation experiments over a ten-year assimilation window, comparing the proposed method, namely profile-by-profile matching, with the traditional method, namely point-by-point matching. The proposed method not only demonstrated a point-by-point skill comparable to the traditional method but also provided superior analysis fields in terms of profile shapes on the temperature-salinity plane. This is an indication of a well-balanced analysis field, in contrast to the traditional method, which can produce extremely poor relative errors for certain metrics. Additionally, signatures were shown to successfully represent properties of the water column, such as steric height, and serve as an effective new diagnostic tool. The top-down, or macro–micro, viewpoint in this method is fundamental to the extent that it can offer an alternative view of how we comprehend ocean observations, holding significant implications for the advancement of data assimilation.