1. A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes
- Author
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Yannick Fourne, Brett W. Engelmann, Zia Khan, John D. Blischak, Michael J. Ford, Chiaowen Joyce Hsiao, and Yoav Gilad
- Subjects
Phosphopeptides ,Proteomics ,0301 basic medicine ,Genotype ,Proteome ,Datasets as Topic ,lcsh:Medicine ,Computational biology ,Biology ,Polymorphism, Single Nucleotide ,Article ,Germline ,03 medical and health sciences ,Tandem Mass Spectrometry ,Cell Line, Tumor ,Stable isotope labeling by amino acids in cell culture ,Humans ,Protein phosphorylation ,Phosphorylation ,Threonine ,lcsh:Science ,Chromatography, High Pressure Liquid ,Multidisciplinary ,Phosphopeptide ,lcsh:R ,Phosphoproteins ,Phenotype ,030104 developmental biology ,Variation (linguistics) ,Biological Variation, Population ,lcsh:Q ,Protein Processing, Post-Translational - Abstract
Phosphorylation of proteins on serine, threonine, and tyrosine residues is a ubiquitous post-translational modification that plays a key part of essentially every cell signaling process. It is reasonable to assume that inter-individual variation in protein phosphorylation may underlie phenotypic differences, as has been observed for practically any other molecular regulatory phenotype. However, we do not know much about the extent of inter-individual variation in phosphorylation because it is quite challenging to perform a quantitative high throughput study to assess inter-individual variation in any post-translational modification. To test our ability to address this challenge with SILAC-based mass spectrometry, we quantified phosphorylation levels for three genotyped human cell lines within a nested experimental framework, and found that genetic background is the primary determinant of phosphoproteome variation. We uncovered multiple functional, biophysical, and genetic associations with germline driven phosphopeptide variation. Variants affecting protein levels or structure were among these associations, with the latter presenting, on average, a stronger effect. Interestingly, we found evidence that is consistent with a phosphopeptide variability buffering effect endowed from properties enriched within longer proteins. Because the small sample size in this ‘pilot’ study may limit the applicability of our genetic observations, we also undertook a thorough technical assessment of our experimental workflow to aid further efforts. Taken together, these results provide the foundation for future work to characterize inter-individual variation in post-translational modification levels and reveal novel insights into the nature of inter-individual variation in phosphorylation.
- Published
- 2018