Protein
localization is paramount to protein function, and the
intracellular movement of proteins underlies the regulation of numerous
cellular processes. Given advances in spatial proteomics, the investigation
of protein localization at a global scale has become attainable. Also
becoming apparent is the need for dedicated analytical frameworks
that allow the discovery of global intracellular protein movement
events. Here, we describe TRANSPIRE, a computational pipeline that
facilitates TRanslocation ANalysis of SPatIal pRotEomics data sets.
TRANSPIRE leverages synthetic translocation profiles generated from
organelle marker proteins to train a probabilistic Gaussian process
classifier that predicts changes in protein distribution. This output
is then integrated with information regarding co-translocating proteins
and complexes and enriched gene ontology associations to discern the
putative regulation and function of movement. We validate TRANSPIRE
performance for predicting nuclear-cytoplasmic shuttling events. Analyzing
an existing data set of nuclear and cytoplasmic proteomes during Kaposi
Sarcoma-associated herpesvirus (KSHV)-induced cellular mRNA decay,
we confirm that TRANSPIRE readily discerns expected translocations
of RNA binding proteins. We next investigate protein translocations
during infection with human cytomegalovirus (HCMV), a β-herpesvirus
known to induce global organelle remodeling. We find that HCMV infection
induces broad changes in protein localization, with over 800 proteins
predicted to translocate during virus replication. Evident are protein
movements related to HCMV modulation of host defense, metabolism,
cellular trafficking, and Wnt signaling. For example, the low-density
lipoprotein receptor (LDLR) translocates to the lysosome early in
infection in conjunction with its degradation, which we validate by
targeted mass spectrometry. Using microscopy, we also validate the
translocation of the multifunctional kinase DAPK3, a movement that
may contribute to HCMV activation of Wnt signaling.