Increasingly, biochemical co-fractionation-based approaches are used to study interactomes and protein complexes at high throughput. The devised methods facilitate the qualitative assignment and prediction of hundreds of putative cellular assemblies in one experiment and without dependency on genetic engineering to introduce affinity tags. The present dataset consists of a native proteome extracted by mild lysis from the HEK293 cell line and fractionated into 80 fractions along high resolution size exclusion chromatography, and each fraction analyzed via bottom-up SWATH mass spectrometry. In multi-tiered targeted analysis, from this fragment ion level chromatographic data, quantitative complex assembly information of the proteome is reconstructed in three steps, (i) peptide-centric detection of peptide analytes within each SEC fraction based on fragment ion co-elution groups; (ii) protein-centric detection of protein elution in SEC based on fragment peptide co-elution groups in SEC; (iii) complex-centric detection and quantification of protein complexes and -variants based on component subunit protein co-elution groups in SEC. The data delineate a global picture of quantitative complex formation within a human proteome, including deconvolution of novel subversions and assembly intermediates of critical cellular complexes with essential functions.