Fig. 2: CFdb prioritizes functional phosphosites and enhances analysis of CF-MS data from non-model organisms.

a Histogram showing the number of phosphoproteins quantified in each CF-MS experiment. b Proportion of phosphoserine (pS), phosphothreonine (pT) and phosphotyrosine (pY) residues in a large-scale meta-analysis of the human phosphoproteome, as compared to all phosphosites detected by CF-MS or phosphosites from the curated PhosphoSitePlus database¹⁶. c Functional scores of human phosphosites that were or were not ever detected by CF-MS (n = 116,258 phosphosites). d Functional scores of human phosphosites, stratified by the number of CF-MS fractions in which each phosphosite was detected (n = 116,258 phosphosites). e Number of phosphosites prioritized based on detection in at least five fractions across major non-human species or taxonomic groups in CFdb. f Example of a frequently quantified phosphosite, pS21 of TPI1. Chromatograms show the intensity of pS21-containing phosphopeptides (green) or the parent protein (light gray). g Overview of understudied human proteins for which an interaction or prioritized phosphosite was detected in CFdb. h Precision of the honey bee CF-MS interactome, inferred with and without a data augmentation strategy that leverages data from hundreds of experiments in CFdb. i Separation of intra- and intra-complex interactions in interactome networks reconstructed for four prokaryotes by random forest classifiers trained in cross-validation on species-specific protein complexes (“within-species”) versus on 206 human and mouse CF-MS experiments (“human/mouse”), as quantified by the area under the ROC curve (AUROC). Source data are provided as a Source Data file.