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Proteomics. 2016 Jul;16(14):2048-58. doi: 10.1002/pmic.201600008.

Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection.

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Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
Department of Chemistry, Northwestern University, Evanston, IL, USA.
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, CA, USA.


Recent studies utilizing transcriptomics, metabolomics, and bottom up proteomics have identified molecular signatures of kidney allograft pathology. Although these results make significant progress toward non-invasive differential diagnostics of dysfunction of a transplanted kidney, they provide little information on the intact, often modified, protein molecules present during progression of this pathology. Because intact proteins underpin diverse biological processes, measuring the relative abundance of their modified forms promises to advance mechanistic understanding, and might provide a new class of biomarker candidates. Here, we used top down proteomics to inventory the modified forms of whole proteins in peripheral blood mononuclear cells (PBMCs) taken at the time of kidney biopsy for 40 kidney allograft recipients either with healthy transplants or those suffering acute rejection. Supported by gas-phase fragmentation of whole protein ions during tandem mass spectrometry, we identified 344 proteins mapping to 2905 distinct molecular forms (proteoforms). Using an initial implementation of a label-free approach to quantitative top down proteomics, we obtained evidence suggesting relative abundance changes in 111 proteoforms between the two patient groups. Collectively, our work is the first to catalog intact protein molecules in PBMCs and suggests differentially abundant proteoforms for further analysis.


Biomarker; Biomedicine; Mass spectrometry; Proteoform; Transplant

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