DOI: 10.5061/dryad.sb669
title: Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs

description: 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 of 27 published and unpublished in-house mass spectrometry–based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.
description: Supplemental Data Set 1.
 Detailed overview of the 27 published p-proteomics studies and unpublished
 in-house data with their respective metadata.SupplementalDataset_1r.xlsxSupplemental 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.xlsxSupplemental 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.xlsxSupplemental Data Set 4. Non-redundant p-15-mers prior to filtering and for sets A and B.SupplementalDataSet_4r.xlsxSupplemental Data Set 5A,B. Analysis of pY peptides (A) and pY proteins (B).SupplementalDataSet_5r.xlsxSupplemental Data Set 6. Published plant p-motifs in various plant species based on motif-x searches against p-proteomics data.SupplementalDataSet_6r.xlsxSupplemental 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.xlsxSupplemental 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.xlsxSupplemental 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 thresholdsSupplementalDataSet_9r.xlsxSupplemental Data Set 10. P-proteins with their p-15-mers and their most significant motifs (from Table 2).SupplementalDataSet_10r.xlsxSupplemental 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.jpegSupplemental 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.jpegSupplemental Figure 2. Kinase recognition motifs for different kinase families in Arabidopsis.SupplementalFigure-2revised.pdf