The sequencing of both the human genome as well as the proteome has given us new perspectives on the complexity of the ‘working parts’ of human biology.  Individual genomes sequencing can give the clinician insights into amino acid polymorphisms as well as gene amplification/mutations which can be related to the development of cancer or to resistance to selected therapies.  Another development has been the deep sequencing of the transcriptome and thus we can now move from the genome to the transcriptome to the proteome.   In fact the best way to assess the consequence of changes at the genome level is to investigate changes in the resulting set of proteins.  Rapid advances in LC/MS have enabled the deeper study of the proteome and for the first time to tackle ‘parts list of the proteome’ in a global collaboration in which different countries study the products of protein coding genes present on a selected individual chromosome.  As an example this lecture will show the integration of the parts list for chromosome 17 in the region of the ERBB2 amplicon that is associated closely with a subset of breast and gastric cancers.   This proteogenomic approach integrates transcriptomic with proteomic information and captures evidence of co-expression through coordinated regulation.  The second part of the lecture will address the challenge of providing protein therapies for an individual or a small subset of patients.  Recent advances in affinity chromatographic approaches and microfluidic devices when coupled to innovations in recombinant DNA based protein manufacture have the potential of enabling the development of individual tailored therapies.  On again LC/MS analysis will play an essential role in the validation of such novel devices and establishing comparability with existing protein therapeutics.