Copepods comprise the majority of mesozooplankton communities in all marine regions. Their diversity is likely regulated by environmental parameters and species-specific ecophysiological aspects making the distributional pattern of certain species an environmental indicator to detect changes in the marine habitat. We studied copepod distribution and diversity at six stations along a meridional transect in the eastern Atlantic Ocean (25°N to 21°S) from surface to 2000 m depths. Community and trophic structures with special regard to calanoid copepods were analyzed. Below the euphotic zone, representatives of the family Spinocalanidae were particularly abundant and diverse but morphological species identification both of adults and juveniles was very challenging. To elucidate both diversity and species- and stage-specific vertical distribution of Spinocalanidae we therefore applied an integrated taxonomic approach combining morphology, DNA sequence analyses and proteomics using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Each specimen was analysed by the three methodologies by portioning the whole organism. Species clusters were similar for DNA sequence analyses and MALDI-TOF MS and resulted in a higher amount of species clusters compared to the morphological identification. Since MALDI-TOF MS is a rather time- and cost-efficient technology, we were able to identify high individual numbers of the Spinocalanidae and received a quantitative, high species-resolution picture of adult and juvenile Spinocalanidae and their distributional patterns.