Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry

Dong Gi Mun; Firdous A. Bhat; Neha Joshi; Leticia Sandoval; Husheng Ding; Anu Jain; Jane A. Peterson; Taewook Kang; Ganesh P. Pujari; Jennifer L. Tomlinson; Rohit Budhraja; Roman M. Zenka; Nagarajan Kannan; Benjamin R. Kipp; Surendra Dasari; Alexandre Gaspar-Maia; Rory L. Smoot; Richard K. Kandasamy; Akhilesh Pandey

doi:10.1038/s42003-024-06579-7

Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry

Dong Gi Mun, Firdous A. Bhat, Neha Joshi, Leticia Sandoval, Husheng Ding, Anu Jain, Jane A. Peterson, Taewook Kang, Ganesh P. Pujari, Jennifer L. Tomlinson, Rohit Budhraja, Roman M. Zenka, Nagarajan Kannan, Benjamin R. Kipp, Surendra Dasari, Alexandre Gaspar-Maia, Rory L. Smoot, Richard K. Kandasamy, Akhilesh Pandey

Research output: Contribution to journal › Article › peer-review

Abstract

The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.

Original language	English (US)
Article number	884
Journal	Communications Biology
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s42003-024-06579-7
State	Published - Dec 2024

ASJC Scopus subject areas

Medicine (miscellaneous)
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

Access to Document

10.1038/s42003-024-06579-7

Cite this

Mun, D. G., Bhat, F. A., Joshi, N., Sandoval, L., Ding, H., Jain, A., Peterson, J. A., Kang, T., Pujari, G. P., Tomlinson, J. L., Budhraja, R., Zenka, R. M., Kannan, N., Kipp, B. R., Dasari, S., Gaspar-Maia, A., Smoot, R. L., Kandasamy, R. K., & Pandey, A. (2024). Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Communications Biology, 7(1), Article 884. https://doi.org/10.1038/s42003-024-06579-7

Mun, DG, Bhat, FA, Joshi, N, Sandoval, L, Ding, H, Jain, A, Peterson, JA, Kang, T, Pujari, GP, Tomlinson, JL, Budhraja, R, Zenka, RM, Kannan, N, Kipp, BR, Dasari, S , Gaspar-Maia, A, Smoot, RL, Kandasamy, RK & Pandey, A 2024, 'Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry', Communications Biology, vol. 7, no. 1, 884. https://doi.org/10.1038/s42003-024-06579-7

@article{ad78c619ab4f4e71bfef4cbcba1207a8,

title = "Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry",

abstract = "The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.",

author = "Mun, {Dong Gi} and Bhat, {Firdous A.} and Neha Joshi and Leticia Sandoval and Husheng Ding and Anu Jain and Peterson, {Jane A.} and Taewook Kang and Pujari, {Ganesh P.} and Tomlinson, {Jennifer L.} and Rohit Budhraja and Zenka, {Roman M.} and Nagarajan Kannan and Kipp, {Benjamin R.} and Surendra Dasari and Alexandre Gaspar-Maia and Smoot, {Rory L.} and Kandasamy, {Richard K.} and Akhilesh Pandey",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",

year = "2024",

month = dec,

doi = "10.1038/s42003-024-06579-7",

language = "English (US)",

volume = "7",

journal = "Communications Biology",

issn = "2399-3642",

publisher = "Springer Nature",

number = "1",

}

TY - JOUR

T1 - Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry

AU - Mun, Dong Gi

AU - Bhat, Firdous A.

AU - Joshi, Neha

AU - Sandoval, Leticia

AU - Ding, Husheng

AU - Jain, Anu

AU - Peterson, Jane A.

AU - Kang, Taewook

AU - Pujari, Ganesh P.

AU - Tomlinson, Jennifer L.

AU - Budhraja, Rohit

AU - Zenka, Roman M.

AU - Kannan, Nagarajan

AU - Kipp, Benjamin R.

AU - Dasari, Surendra

AU - Gaspar-Maia, Alexandre

AU - Smoot, Rory L.

AU - Kandasamy, Richard K.

AU - Pandey, Akhilesh

PY - 2024/12

Y1 - 2024/12

N2 - The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.

AB - The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.

UR - http://www.scopus.com/inward/record.url?scp=85199188539&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85199188539&partnerID=8YFLogxK

U2 - 10.1038/s42003-024-06579-7

DO - 10.1038/s42003-024-06579-7

M3 - Article

C2 - 39030393

AN - SCOPUS:85199188539

SN - 2399-3642

VL - 7

JO - Communications Biology

JF - Communications Biology

IS - 1

M1 - 884

ER -

Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this