In the field of microbiology, identifying and comparing species of bacteria from large communities is commonplace. Traditionally, this has been achieved by DNA sequence analysis of isolates and/or metagenomics, but this is a time-intensive and potentially costly process. Microbial analysis via mass spectroscopy can be an effective and accurate process for preliminary analysis, as well as significantly faster and less expensive. We have developed a software package, HTMAD (³hat-mad²), to process datasets of spectra from MALDI-TOF mass spectroscopy and to provide analysis. In particular, we are using this process to identify prophage-infected bacteria and for dereplication of bacteria across multiple treatment groups.