Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling.

By K. Sharma, Rochelle C. J. D’Souza, Stefka Tyanova, Christoph Schaab, Jacek R. Wisniewski, Jüergen Cox, Matthias Mann. Cell Reports, 2014

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Regulatory protein phosphorylation controls normal and pathophysiological signaling in eukaryotic cells. Despite great advances in mass-spectrometry-based proteomics, the extent, localization, and site-specific stoichiometry of this posttranslational modification (PTM) are unknown. Here, we develop a stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. We detected more than three-quarters of cellular proteins as phosphoproteins and determined very high stoichiometries in mitosis or growth factor signaling by label-free quantitation. The proportion of phospho-Tyr drastically decreases as coverage of the phosphoproteome increases, whereas Ser/Thr sites saturate only for technical reasons. Tyrosine phosphorylation is maintained at especially low stoichiometric levels in the absence of specific signaling events. Unexpectedly, it is enriched on higher-abundance proteins, and this correlates with the substrate KM values of tyrosine kinases. Our data suggest that P-Tyr should be considered a functionally separate PTM of eukaryotic proteomes.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/932384f9ee5b59366b0ba8bd77e3c5e5d50998e1

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Citations in the corpus

MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics (2017, methodology): “To demonstrate this, in addition to the HEK293 data set, we also probed HeLa 37 and triple-negative breast cancer (TNBC) 38 proteome-wide data sets using open searches and compared their modification profiles (Online Methods and Supplementary Table 2 ).”
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics (2016, methodology): “Site occupancies can then be calculated when, in addition to the PTM-enriched samples, the full proteomes have been measured as well 25 .”
Multidimensional proteomics for cell biology (2015, background): “These studies have provided crucial insights into the regulation of protein properties during fundamental processes, such as cell cycle progression 83,84 , and into signalling mechanisms that affect cellular pathways, such as the epidermal growth factor signalling cascade 85 .”
The functional landscape of the human phosphoproteome (2019, methodology): “The phospho-deficient mutant binding remained similar to the WT in the case of RAN and RCC1 but showed a reproducible decrease (p < 0.003) in binding capability to NEMP1, an interaction partner previously described in other eukaryotes (Figure 3c) (Shibano et al. 2015).”
Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases (2016, background): “With current MS instrumentation, proteomics can identify tens of thousands of phosphosites (Sharma et al., 2014; Mallick and Kuster, 2010).”