A tissue-specific atlas of mouse protein phosphorylation and expression
Open accessAbstract
Although most tissues in an organism are genetically identical, the biochemistry of each is optimized to fulfill its unique physiological roles, with important consequences for human health and disease. Each tissue's unique physiology requires tightly regulated gene and protein expression coordinated by specialized, phosphorylation-dependent intracellular signaling. To better understand the role of phosphorylation in maintenance of physiological differences among tissues, we performed proteomic and phosphoproteomic characterizations of nine mouse tissues. We identified 12,039 proteins, including 6296 phosphoproteins harboring nearly 36,000 phosphorylation sites. Comparing protein abundances and phosphorylation levels revealed specialized, interconnected phosphorylation networks within each tissue while suggesting that many proteins are regulated by phosphorylation independently of their expression. Our data suggest that the "typical" phosphoprotein is widely expressed yet displays variable, often tissue-specific phosphorylation that tunes protein activity to the specific needs of each tissue. We offer this dataset as an online resource for the biological research community.
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S239 was identified as an in vivo ATXN1 phosphorylation site in multiple tissues, including brain, by mass-spectrometry analysis.
“One of these sites is serine 239 (S239), which was identified as an in vivo ATXN1 phosphorylation site in multiple tissues, including brain, by mass-spectrometry analysis (Vierra-Green et al., 2005; Huttlin et al., 2010).”
From Polyglutamine Disease Toxicity Is Regulated by Nemo-like Kinase in Spinocerebellar Ataxia Type 1 (2013) · cites this paper as Huttlin et al., 2010
The Experimental Procedures describe LC-MS/MS analysis of phosphopeptides from nine mouse organs, including brain, and the Results discuss phosphorylation across tissues. But our copy does not identify ATXN1 S239 or say that this site was found in multiple tissues; searches for ATXN1, ataxin-1, and S239 found no matching passage. (LLM, conf=0.72)
Experimental — accuracy not yet measuredIn SCA1, several phosphorylation sites have been identified in mouse brain in vivo including S776 and S239.
“In SCA1, several phosphorylation sites have been identified so far in mouse brain in vivo including S776 and S239 (Emamian et al., 2003; Vierra-Green et al., 2005; Huttlin et al., 2010).”
From Polyglutamine Disease Toxicity Is Regulated by Nemo-like Kinase in Spinocerebellar Ataxia Type 1 (2013) · cites this paper as Huttlin et al., 2010
The Results section on tissue distribution reports phosphorylation sites in mouse brain, but the passages from our copy do not identify SCA1/ataxin-1 sites S776 or S239. Searches for those site numbers, ataxin-1/Atxn1, and spinocerebellar ataxia found no passage addressing the specific claim; page numbers were not provided. (LLM, conf=0.72)
Experimental — accuracy not yet measuredSignificantly higher numbers of identified proteins were so far only achieved by combining multiple diverse cell lines or tissues in one analysis, or by investing weeks of measurement for single samples.
“Significantly higher numbers of identified proteins were so far only achieved by combining multiple diverse cell lines or tissues in one analysis (11), or by investing weeks of measurement for single samples (12, 13).”
From Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins (2012) · cites this paper as [11]
The dataset was filtered to an MS2 spectra assignment false discovery rate of smaller than 1% at the protein level, using probabilities from linear discrimination scores.
“Linear discrimination scores were used to assign probabilities to each MS2 spectrum for being assigned correctly and these probabilities were further used to filter the dataset with an MS2 spectra assignment FDR of smaller than a 1% at the protein level58.”
From Identification of a unique TGF-β–dependent molecular and functional signature in microglia (2014) · cites this paper as [58]
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Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids
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Amino Acid-Dependent mTORC1 Regulation by the Lysosomal Membrane Protein SLC38A9
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Age-induced accumulation of methylmalonic acid promotes tumour progression
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Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics
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Self-citationInitial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse
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eIF2B activator prevents neurological defects caused by a chronic integrated stress response
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Parkin-catalyzed Ubiquitin-Ester Transfer Is Triggered by PINK1-dependent Phosphorylation
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Essential metabolism for a minimal cell
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“Peptides matching to multiple proteins were assigned to the protein containing the largest number of matched redundant peptides following the law of parsimony (Huttlin et al., 2010).”
BackgroundTissue-Specific Oncogenic Activity of KRASA146T
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Self-citationTargeted degradation of the enhancer lysine acetyltransferases CBP and p300
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Self-citationPARP1 inhibitors trigger innate immunity via PARP1 trapping-induced DNA damage response
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The Revolution and Evolution of Shotgun Proteomics for Large-Scale Proteome Analysis
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“The samples were fractionated into 96 fractions, then pooled into 12 fractions as previously described ( Huttlin et al., 2010 ).”
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Molecular basis for substrate recruitment to the PRMT5 methylosome
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“One of these sites is serine 239 (S239), which was identified as an in vivo ATXN1 phosphorylation site in multiple tissues, including brain, by mass spectrometry analysis (Vierra-Green et al., 2005; Huttlin et al., 2010).”
BackgroundPost-translational modifications of the mitochondrial F 1 F O -ATPase
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LKB1 regulates JNK-dependent stress signaling and apoptotic dependency of KRAS-mutant lung cancers
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“Each MS2 spectra was assigned using a SEQUEST-based custom proteomics analytical pipeline 89 allowing phosphorylation of tyrosine, threonine, and serine residues as a variable mod-i fi cation.”
InfluentialSelf-citation
- Authors
- Huttlin, E. L., Jedrychowski, M. P., Elias, J. E., Goswami, T., Rad, R., Beausoleil, S. A., Villén, J., Haas, W., Sowa, M. E., & Gygi, S. P.
- Affiliations
- Harvard University (US)
- Corresponding author
- Gygi, Steven P.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2010-12
- Volume
- 143
- Issue
- 7
- Pages
- 1174-1189
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3035969
- OpenAlex
- W2123347941
- Cited by
- 1,778
- References
- 65
- Citations by year
- 2026: 74 · 2025: 112 · 2024: 132 · 2023: 104 · 2022: 90 · 2021: 118 · 2020: 150 · 2019: 130 · 2018: 113 · 2017: 123 · 2016: 107 · 2015: 116 · 2014: 115 · 2013: 118 · 2012: 117
- FWCI
- 43.01
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (HG3456, R01HG003456)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
- Keywords
- protein phosphorylation, phosphoproteomics, protein expression, mouse tissues, phosphorylation sites, phosphorylation networks, intracellular signaling, tissue physiology, protein abundance
- MeSH terms
- Animals, Organ Specificity, Phosphorylation, Protein Kinases, Proteins, Gene Expression Profiling, Proteomics, Mice
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