# InducibleHIV_Fractionation
GitHub repository for "Proteomic Organellar Mapping Identifies Modulation of Peroxisomes by HIV-1" (Oom et al, 2021).

Example code is included here for wild-type biological replicate 2 with specific technical replicate code for Uninduced A. Jupyter notebooks comparing biological replicates for WT and dNef can be found in the respective folders. Notebooks in the main folder start with splitting out individual replicates from full mass spec data (Ntbk1), then normalize proteins by row sum (Ntbk2), identify marker proteins (Ntbk3), remove outlier markers (Ntbk4), and then classify an individual technical replicate (Ntbk6); concordance of marker behavior across individual technical replicates is also shown (Ntbk5). Following classification, proteins can be reverted to unclassified if they have a low-confidence assignment (Ntbk7). Lastly, significant movement of proteins in a given biological replicate is determined using a centroid-based analysis (Ntbk8). Additionally, notebooks for all main figures have been included to show code used in generating each.

Raw data for all analyses can be found in the RawData folder.

All classification was performed on the San Diego Supercomputing Center's Comet supercomputer using a full node (~128Gb of RAM) for recursive classification of a single technical replicate.

Maintained by ALO (aoom@health.ucsd.edu)