*Purpose: Transcriptomics analyses have not generated reliable means to distinguish T-cell mediated rejection (TCMR) from BK virus nephropathy (BKVN). Proteomics-based approaches deserve further exploration since these encompass additional layers of gene regulation that may not be reflected in transcript abundance.

*Methods: 15 formalin-fixed paraffin-embedded (FFPE) kidney biopsies with normal histology, TCMR or BKVN were subjected to protein extraction, acetone precipitation, reduction, alkylation, in-solution digestion, TMT 10-plex isobaric mass tag labeling, loss-less basic reverse phase fractionation, and LC-MS/MS analysis in triplicate. Data analysis consisted of reporter ion intensity relative quantification, log transformation, quantile normalization, and differential expression (DE) analysis by Limma.

*Results: The comparison of TCMR and BKVN samples revealed 218 DE proteins (FDR<0.05) in a combined dataset. 27 were present in all replicates and changed in a consistent direction: 13 increased in TCMR and 14 in BKVN. Pathway analysis revealed differences in proteins relevant to the viral life cycle including clathrin mediated endocytosis related to intracellular virus entry and EIF2 signaling pertinent to BKV replication. 224 and 256 proteins showed consistent DE between TCMR versus normal and BKVN versus normal biopsies, respectively. Virus-encoded proteins VP-1 and LTA were demonstrable in samples with BKVN. Genes encoding several of these proteins were not identified in prior microarray or RNA-seq studies, suggesting differential regulation independent of transcriptional control.

*Conclusions: TMT-based quantitative proteomic analyses offers novel means to (i) simultaneously assess the relative contributions of TCMR and BKVN in biopsy tissue, and (ii) discover novel host therapeutic targets to curtail productive BKV infection.

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