Mass spectrometry-based draft of the mouse proteome

Piero Giansanti; Patroklos Samaras; Yangyang Bian; Chen Meng; Andrea Coluccio; Martin Frejno; Hannah Jakubowsky; Sophie Dobiasch; Rashmi R. Hazarika; Julia Rechenberger; Julia Calzada-Wack; Johannes Krumm; Sebastian Mueller; Chien Yun Lee; Nicole Wimberger; Ludwig Lautenbacher; Zonera Hassan; Yun Chien Chang; Chiara Falcomatà; Florian P. Bayer; Stefanie Bärthel; Tobias Schmidt; Roland Rad; Stephanie E. Combs; Matthew The; Frank Johannes; Dieter Saur; Martin Hrabe de Angelis; Mathias Wilhelm; Günter Schneider; Bernhard Kuster

doi:10.1038/s41592-022-01526-y

Mass spectrometry-based draft of the mouse proteome

Piero Giansanti, Patroklos Samaras, Yangyang Bian, Chen Meng, Andrea Coluccio, Martin Frejno, Hannah Jakubowsky, Sophie Dobiasch, Rashmi R. Hazarika, Julia Rechenberger, Julia Calzada-Wack, Johannes Krumm, Sebastian Mueller, Chien Yun Lee, Nicole Wimberger, Ludwig Lautenbacher, Zonera Hassan, Yun Chien Chang, Chiara Falcomatà, Florian P. BayerStefanie Bärthel, Tobias Schmidt, Roland Rad, Stephanie E. Combs, Matthew The, Frank Johannes, Dieter Saur, Martin Hrabe de Angelis, Mathias Wilhelm, Günter Schneider, Bernhard Kuster

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Abstract

The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.

Original language	English
Pages (from-to)	803-811
Number of pages	9
Journal	Nature Methods
Volume	19
Issue number	7
DOIs	https://doi.org/10.1038/s41592-022-01526-y
State	Published - Jul 2022

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Giansanti, P., Samaras, P., Bian, Y., Meng, C., Coluccio, A., Frejno, M., Jakubowsky, H., Dobiasch, S., Hazarika, R. R., Rechenberger, J., Calzada-Wack, J., Krumm, J., Mueller, S., Lee, C. Y., Wimberger, N., Lautenbacher, L., Hassan, Z., Chang, Y. C., Falcomatà, C., ... Kuster, B. (2022). Mass spectrometry-based draft of the mouse proteome. Nature Methods, 19(7), 803-811. https://doi.org/10.1038/s41592-022-01526-y

@article{86c63b656ee140e485741197ebb90c1a,

title = "Mass spectrometry-based draft of the mouse proteome",

abstract = "The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.",

author = "Piero Giansanti and Patroklos Samaras and Yangyang Bian and Chen Meng and Andrea Coluccio and Martin Frejno and Hannah Jakubowsky and Sophie Dobiasch and Hazarika, {Rashmi R.} and Julia Rechenberger and Julia Calzada-Wack and Johannes Krumm and Sebastian Mueller and Lee, {Chien Yun} and Nicole Wimberger and Ludwig Lautenbacher and Zonera Hassan and Chang, {Yun Chien} and Chiara Falcomat{\`a} and Bayer, {Florian P.} and Stefanie B{\"a}rthel and Tobias Schmidt and Roland Rad and Combs, {Stephanie E.} and Matthew The and Frank Johannes and Dieter Saur and {de Angelis}, {Martin Hrabe} and Mathias Wilhelm and G{\"u}nter Schneider and Bernhard Kuster",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2022",

month = jul,

doi = "10.1038/s41592-022-01526-y",

language = "English",

volume = "19",

pages = "803--811",

journal = "Nature Methods",

issn = "1548-7091",

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Giansanti, P, Samaras, P, Bian, Y, Meng, C, Coluccio, A, Frejno, M, Jakubowsky, H, Dobiasch, S, Hazarika, RR, Rechenberger, J, Calzada-Wack, J, Krumm, J, Mueller, S, Lee, CY, Wimberger, N, Lautenbacher, L, Hassan, Z, Chang, YC, Falcomatà, C, Bayer, FP, Bärthel, S, Schmidt, T, Rad, R , Combs, SE, The, M, Johannes, F , Saur, D, de Angelis, MH, Wilhelm, M, Schneider, G & Kuster, B 2022, 'Mass spectrometry-based draft of the mouse proteome', Nature Methods, vol. 19, no. 7, pp. 803-811. https://doi.org/10.1038/s41592-022-01526-y

TY - JOUR

T1 - Mass spectrometry-based draft of the mouse proteome

AU - Giansanti, Piero

AU - Samaras, Patroklos

AU - Bian, Yangyang

AU - Meng, Chen

AU - Coluccio, Andrea

AU - Frejno, Martin

AU - Jakubowsky, Hannah

AU - Dobiasch, Sophie

AU - Hazarika, Rashmi R.

AU - Rechenberger, Julia

AU - Calzada-Wack, Julia

AU - Krumm, Johannes

AU - Mueller, Sebastian

AU - Lee, Chien Yun

AU - Wimberger, Nicole

AU - Lautenbacher, Ludwig

AU - Hassan, Zonera

AU - Chang, Yun Chien

AU - Falcomatà, Chiara

AU - Bayer, Florian P.

AU - Bärthel, Stefanie

AU - Schmidt, Tobias

AU - Rad, Roland

AU - Combs, Stephanie E.

AU - The, Matthew

AU - Johannes, Frank

AU - Saur, Dieter

AU - de Angelis, Martin Hrabe

AU - Wilhelm, Mathias

AU - Schneider, Günter

AU - Kuster, Bernhard

PY - 2022/7

Y1 - 2022/7

N2 - The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.

AB - The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.

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U2 - 10.1038/s41592-022-01526-y

DO - 10.1038/s41592-022-01526-y

M3 - Article

C2 - 35710609

AN - SCOPUS:85132394242

SN - 1548-7091

VL - 19

SP - 803

EP - 811

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

Mass spectrometry-based draft of the mouse proteome

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