The fields of proteogenomics/proteotranscriptomics combine data from genomic sequencing, gene expression analysis and mass-spectrometry (MS) proteomics analysis to enable a more complete view on the biology of the analysed samples. Our projects utilise the in-house MS-proteomics capabilities of Johan Malmströms group at the biomedical centre at Lunds University (BMC), the sequencing facilities of the Center for Translational Genomics (CTG) for RNA and whole exome sequencing (WES) as well as Sci-life-lab in Uppsala for whole genome sequencing (WGS) to implement a multi-omics view of our sample sets. Our aim is to establish workflows for the analysis of RNA, WES and WGS data and develop methods to combine this data with MS-proteomics results in a multi-omics analysis. The workflows for the analysis of genomic/transcriptomics and proteomics data independently are based on published software that is available and widely accepted in the scientific community. The combination of such results in a multi-omics analysis is a rapidly evolving field of research and developing and publishing methods in this field will both allow us to establish proteogenomics as a core competence of our group and give us the opportunity to make an impact on the way such analyses are performed through contribution of open-source software packages that we will develop in our projects.