Proteogenomics is an interdisciplinary research area of proteomics and genomics. Recent advancements in high-throughput sequencing technologies such as RNA-seq have brought dynamic improvements in analyzing high-resolution mass spectrometry data. At YU-IOB-CSBMM, we are developing various proteogenomic pipelines using the in house generated mass spectrometry data derived from various biological specimens such as medically important fungi and bacteria. Spectra will be searched against the six frame translated genome or three frame translated transcriptome data. The analysis will allow the identification of novel proteins as well as to re-annotate the existing gene models. We are currently performing proteogenomics analysis of several emerging opportunistic pathogens.