Citation
van Wijk, Klaas J.; Friso, Giulia; Walther, Dirk; Schulze, Waltraud X. (2014), Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs, Dryad, Dataset, https://doi.org/10.5061/dryad.sb669
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry–based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
Supplemental Data Set 1. Detailed overview of the 27 published p-proteomics studies and unpublished in-house data with their respective metadata.
SupplementalDataset_1r.xlsx
Supplemental Data Set 2. The complete unfiltered set of 60366 p-peptides with matched protein id, their metadata, p-15-mers, annotation from PPDB, SUBA3 consensus prediction and assignment to one of seven locations.
SupplementalDataSet_2rfinal.xlsx
Supplemental Data Set 3. Non-redundant Arabidopsis p-proteins before filtering (8141 proteins) or after filters 1&2 (set A – 4494 proteins) and after filters 1,2,3,4 (set B -3687 proteins) with their annotations.
SupplementalDataSet_3r.xlsx
Supplemental Data Set 4. Non-redundant p-15-mers prior to filtering and for sets A and B.
SupplementalDataSet_4r.xlsx
Supplemental Data Set 5A,B. Analysis of pY peptides (A) and pY proteins (B).
SupplementalDataSet_5r.xlsx
Supplemental Data Set 6. Published plant p-motifs in various plant species based on motif-x searches against p-proteomics data.
SupplementalDataSet_6r.xlsx
Supplemental Data Set 7. P-motifs for pS, pT and pY and their fold-enrichment in sets A and B, and the localization of p-15-mer sets using motif-x at the 10-6 threshold and 1%, 3% and 5% occurrence rates.
SupplementalDataSet_7r.xlsx
Supplemental Data Set 8. P-motifs for pS, pT and pY in sets A and B and the localization of p-15-mer sets using MMFPh at the 10-6 threshold and 1%, 5% and 10% occurrence rates.
SupplementalDataSet_8r.xlsx
Supplemental Data Set 9. Motifs for pS, pT and pY found by motif-x and MMFPh for sets A and B and subcellular sets at all occurrence thresholds
SupplementalDataSet_9r.xlsx
Supplemental Data Set 10. P-proteins with their p-15-mers and their most significant motifs (from Table 2).
SupplementalDataSet_10r.xlsx
Supplemental Figure 1A. Hierarchical clustering (average linkage method) of all 364 non-redundant pS motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
SupplementalFigure_1A.jpeg
Supplemental Figure 1B. Hierarchical clustering (average linkage method) of all 26 non-redundant pT motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
SupplementalFigure_1B.jpeg
Supplemental Figure 2. Kinase recognition motifs for different kinase families in Arabidopsis.
SupplementalFigure-2revised.pdf