Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry

Author:

Su Pei1ORCID,McGee John P.1ORCID,Durbin Kenneth R.1ORCID,Hollas Michael A. R.1ORCID,Yang Manxi2ORCID,Neumann Elizabeth K.3ORCID,Allen Jamie L.3ORCID,Drown Bryon S.1ORCID,Butun Fatma Ayaloglu4,Greer Joseph B.1ORCID,Early Bryan P.1,Fellers Ryan T.1ORCID,Spraggins Jeffrey M.35ORCID,Laskin Julia2ORCID,Camarillo Jeannie M.14ORCID,Kafader Jared O.14ORCID,Kelleher Neil L.146ORCID

Affiliation:

1. Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA.

2. Department of Chemistry, Purdue University, West Lafayette, IN, USA.

3. Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.

4. Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.

5. Departments of Chemistry and Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.

6. Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.

Abstract

Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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