The characterization and engineering of monoclonal antibodies is usually preceded by time-consuming Edman/cDNA sequencing steps for determination of the heavy and light chain sequences – a low-throughput pipeline that does not address post-translational modifications. In a departure from these platforms, we have developed the Comparative Shotgun Protein Sequencing (CSPS) suite of algorithms – a mass spectrometry based protein sequencing approach resulting in over 95% sequence coverage and automatic discovery of unexpected post-translational modifications. In contrast with the current multiple-week duration of typical sequencing projects, CSPS delivers additional functionality while reducing the time required to sequence an antibody to under 72 hours, a dramatic reduction as compared to the average 2-4 months for classical Edman sequencing of an entire antibody. While we demonstrate CSPS on monoclonal antibodies, the underlying techniques are not antibody-specific and the results indicate that CSPS has the potential to be a disruptive technology for all protein sequencing applications.