Fig. 3: Composition of the reference spectral library for the global phosphoproteome system. | Nature Communications

Fig. 3: Composition of the reference spectral library for the global phosphoproteome system.

From: A data-independent acquisition-based global phosphoproteomics system enables deep profiling

Fig. 3

a Proteome and phosphoproteome libraries composition and protein groups overlap. b Phosphopeptides in hybrid and DDA-only libraries. c Distribution of phosphorylated serine (pSer), threonine (pThr), and tyrosine (pTyr) in the global phosphoproteome system (GPS) library. d Pathway annotation of phosphoproteins in the library using Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The circle size corresponds to phosphosite coverage, whereas the X and Y axis shows protein coverage in the pathway and size of protein, respectively. The number in the circles shows number of phosphosites covered in the pathway. The blue color intensity shows the percentage of pathway coverage. e Kinase tree revealed 383 kinases in the library with proportion of each kinase family covered shown in bracket. KinMap database (http://www.kinhub.org/kinmap/) was used with input of protein accession number from GPS library. The kinase families listed includes TK (tyrosine kinases), TKL (tyrosine kinase-like), CK1 (casein kinase 1), CAMK (calcium/calmodulin-dependent protein kinase), AGC (containing PKA, PKG, PKC families), CMGC (containing CDKs, MAPK, GSK, CLK families), and STE (serine/threonine kinases many involved in MAPK kinases cascade). f Phosphatase obtained mapping to human dephosphorylation database (DEPOD) (www.depod.org). A total of 140 phosphatases were included in the library with the top ten families shown. The phosphatase family abbreviated are RPTPs (receptor protein tyrosine phosphatases), nRPTPs (nonreceptor-type protein tyrosine phosphatases), MKPs (MAPK phosphatases), aDSPs (Atypical DSPs), MTM (Myotubularins), PPM (protein phosphatase Mg2+ or Mn2+ dependent), FCP/SCP (TFIIF-associating component of RNA polymerase II CTD phosphatase/small CTD phosphatase), PAP (Phosphatidic acid phosphatase), INPP5 (Inositol-1,4,5-trisphosphate 5-phosphatase), and PGAM (Phosphoglycerate mutase). Source data are provided as a Source Data file.

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