Updated project metadata. We attempted to increase proteome and protein sequence coverage in MCF-7 breast cancer cells using CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion Lumos mass spectrometer. The parallel use of both detectors available in this instrument, orbitrap and linear iontrap, to generate MS/MS spectra on selected precursor ions allowed a significantly increased success rate for spectrum identification as compared to a “Universal” method, which uses orbitrap for precursor and linear ion trap for MS/MS detection in a separate fashion. Consequently, CHOPIN resulted in higher peptide and protein scores, resulting in an increased confidence of identification. Overall, using high pH based pre-fractionation, we generated 3,517,223 MS/MS spectra and identified 19,803 protein groups (including isoforms) with a total of 535,882 unique peptides, representing 9,906 Ensembl gene IDs in MCF-7 cells with a mean sequence coverage of 32%. More than 5,000 protein groups could be detected with a sequence coverage of >50% allowing to map 206 different modifications to a total of 38.895 sites in 14,434 proteins, thereby covering the deep proteome in unprecedented detail.