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Mass spectrometry proteomic data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD015993.
All code to reproduce the analysis and figures is available at https://github.com/nkurzaw/phosphoTPP.
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This work was supported by the European Molecular Biology Laboratory. C.M.P. and A.M. were supported by a fellowship from the EMBL Interdisciplinary Postdoctoral (EI3POD) Programme under Marie Skłodowska-Curie Actions COFUND (grant number 664726). N.K. was supported by a fellowship from the EMBL International PhD Programme.
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Supplementary Discussion, Figs. 1–11 and Table 1
Phosphopeptide fold changes at each temperature in each replicate (gene_name, gene name; protein_id, UniProt ID; sequence, peptide sequence; mod_sequence, modified peptide sequence; phospho_site_STY, number of modified amino acids in the peptide sequence; rel_fc_TMT_REP_TEMP, relative fold changes to 37 °C (TMT, TMT label; REP, replicate; TEMP, temperature).
Unmodified peptide fold changes at each temperature in each replicate (gene_name, gene name; protein_id, UniProt ID; sequence, peptide sequence; modifications, peptide modifications; rel_fc_TMT_REP_TEMP, relative fold changes to 37 °C (TMT, TMT label; REP, replicate; TEMP, temperature).
Comparison of melting behavior of phosphopeptides and unmodified peptides (gene_name, gene name; Gene_pSite, phosphosite position within protein; mod_sequence, modified peptide sequence; Tm_mean_phospho, average melting temperature of phosphopeptide; Tm_mean_unmodified, average melting temperature of unmodified protein; mean_delta_meltPoint, average difference of melting temperature of phosphopeptide and unmodified protein; significant, significantly different melting temperature of phosphopeptide compared to unmodified protein; functional_score, predicted functional importance of phosphosite position by aggregating multiple parameters for each phosphosite using machine learning and ranges from 0 to 1, with a higher value representing a higher probability that the phosphosite has functional relevance; Tm_phospho_REP, melting temperature of phosphopeptide (REP, replicate); Tm_unmodified_REP, melting temperature of unmodified protein; delta_meltPoint_REP, difference of melting temperature of phosphopeptide and unmodified protein; p_adj_REP, P value adjusted for multiple-testing correction; phospho_median_fc_TEMP, median relative fold changes to 37 °C of phosphopeptide (TEMP, temperature); unmodified_median_fc_TEMP, median relative fold changes to 37 °C of unmodified protein.
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Potel, C.M., Kurzawa, N., Becher, I. et al. Impact of phosphorylation on thermal stability of proteins. Nat Methods 18, 757–759 (2021). https://doi.org/10.1038/s41592-021-01177-5
Nature Methods (2021)