Survey of phosphorylation motifs

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binding sites 58 of the 473 unambiguously assigned phosphorylation sites are predicted by Scansite to be sites for binding. 50 of these correspond.

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Correlation of log-transformed signal intensity from two Affymetrix microarray hybridizations using platelet RNA. Plotted are those probesets with an average.

Sequence alignment of C-terminal phosphorylated plant aquaporins

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z ).

Distribution of disorder in the cytosolic phosphoproteome

Phosphorylation and sequence disorder in microtubule-associated protein Tau.A, schematic illustration of the domain profile of Tau with all known phosphorylation.

Distribution of phosphorylation sites identified in the cytosolic phosphoproteome.A, numbers of approved phosphopeptides, previously phosphorylated peptides,

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;4.A, MS/MS spectrum of singly phosphorylated 277ALGSFGSFGSFRSFA291 (m/z ).

Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;7.A, MS/MS spectrum of singly phosphorylated 270ALGSFRSNATN280 (m/z ).

Phosphopeptides identified harboring minimal binding motifs

Percentage of proteins identified in envelope membrane extracts according to the purification method and the number of transmembrane domains. Percentage.

Novel phosphorylation sites on H+-ATPase proteins

A, high resolution MS/MS spectrum (lower panel) of 1435

Illustration of matched (FL-IFN-γR2/GFP and IFN-γR1/EBFP) and mismatched (IFN-γR1/EBFP and FL-IL-10R2/GFP) pairs of receptors. Illustration of matched.

Phosphorylation reduces peptide solution charge state and alters SCX elution at low pH.A, at pH 2.7, a theoretical tryptic peptide without histidine residues.

Frequency distribution of the GRAVY of the theoretical proteins (open bars) and of 110 genes encoding proteins identified on a 2-D electrophoresis gel,

Time course of phosphorylation changes at Ser-293, Ser-300, and Ser-232 in PDHE1α following kinase inhibition with DCA. A, relative quantitation over three.

Distributions of the ELDP values and Mascot scores for all protein identifications.a, frequency of ELDP value returned by correct (gray bars) and incorrect.

Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. Significantly enriched phosphorylation motifs from.

Visual validation of the computational outputs.

Novel p53 target genes identified by RNA-Seq, pSILAC and ChIP-Seq.

Assay of NOS activity. Assay of NOS activity. Box show total NOS activity, the calcium-dependent activity of the constitutive isoforms of NOS (eNOS and.

Comparison of ROC plots for the PMF quality metrics using test dataset 2 (44 C. difficile proteins).a, ROC curves for coverage (open squares), MC (solid.

Success rates in validation of antibodies from external providers

Results from the Morris water task.

Degree of glycosylation of human milk LF from individual donors across lactation. Degree of glycosylation of human milk LF from individual donors across.

Correction of translational start site by identification of N-terminal peptide. Correction of translational start site by identification of N-terminal.

The evolutionary conservation of the phosphoproteomes.a, E. coli. b, B. subtilis. The evolutionary conservation of the phosphoproteomes.a, E. coli. b,

BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere cells. BIRC6 is expressed in the tumorigenic Aldefluorhigh fraction of colonosphere.

Colonopshere-enriched proteins display functional interactions.

Identification of SUMO3peptides from 2D-LC-MS/MS analyses of a tryptic digest of HEK293-SUMO3 cells using DDA and DIA methods. Identification of SUMO3peptides.

Comparison of ROC plots for the PMF quality metrics using test dataset 3 (100 M. jannaschii proteins).a, ROC curves for coverage (open squares), MC (solid.

Proteins previously reported in published MALDI IMS studies and their frequency of observation in the present study. Proteins previously reported in published.

N-terminal extension of a gene using peptides mapping upstream to an annotated start site. N-terminal extension of a gene using peptides mapping upstream.

MS/MS spectra of INEILSNALKR with a Lys residue modified with SUMO1 or SUMO3 remnant chains. MS/MS spectra of INEILSNALKR with a Lys residue modified with.

Testing the effectiveness of the three-step peptide fractionation method.A, μLC mass chromatograms of SCX fractions for an acidic FFE fraction. Testing.

Altered pathways in prostate cancer.

Resolution and mass accuracy of A, a peptide isotope cluster (m/z 558

Interaction networks of the regulated phosphoproteins.

The PPAR-α agonist GW7647 reduces experimentally induced myopia.

Overview of the analytical workflow used in this study and a representative MS/MS spectrum.a, Overview of the analytical workflow used in this study. Overview.

Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum. Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum.A,

Plot of the deviation of the predicted pI value of every peptide spectrum from the average pI calculated for each fraction for validated (a) and non-validated.

Distribution of the phosphoproteins based on GO analysis, including biological process (Left) and cellular component (Right). Distribution of the phosphoproteins.

Significant alterations in cysteine and methionine metabolism.

Number of genes/antibodies included in the database.

Immuno-MS results from antibodies toward 20 different target proteins in HeLa cell lysates. Immuno-MS results from antibodies toward 20 different target.

Phylogenetic trees of the closest eukaryotic homologs of clones AY and AY Phylogenetic trees of the closest eukaryotic homologs of clones.

Biochemical characterization of the protein phosphatases Saci-PP2A.

Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry. Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry.

Image analysis and HER-2/neu slide scoring.

Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.

Separation of colonospheres from differentiated tumor cells by cluster analysis. Separation of colonospheres from differentiated tumor cells by cluster.

Comparison of HCT-8 cell line proteome under apoptotic conditions in response to 10 mm Gln treatment Spot numbers with corresponding Swiss-Prot database.

Expression of σ in SCCs Expression of σ in SCCs. Shown is a magnified section of a representative 2D PAGE gel run with a lysate from an SCC.

Antibody specificity ascertained by 2D-PAGE Western immunoblotting (IEF) of total cellular protein extracts from the RT4 human bladder cancer cell line.

SDS-PAGE of IGFBP-5 from 32P-labeled T47D cells and separation of tryptic phosphopeptides separated by HPLC.a, an autoradiograph (lane 1) is shown next.

Eight serum proteins (P-selectin, E-selectin, IL-2sRα, IL-18, NE, uPA, uPAR, and CRP) that are elevated in infected neonates function in a molecular network.

Proteomics analysis of NaPi-IIa C terminus binding to PDZ proteins.

Tryptic phosphopeptides of 32P-labeled IGFBP-5 from T47D cells separated by HPLC and sequenced by tandem MS.a, tandem MS spectrum of the triply charged.

Tryptic glycopeptides of IGFBP-5 from T47D cells separated by HPLC detected by ESI-MS and sequenced by tandem MS.a, ESI-MS spectrum of combined fractions.

Eight serum analytes with greatest differences in levels between clinically infected and non-infected neonates. Eight serum analytes with greatest differences.

Changes in protein expression during distinct stages of NK cell differentiation. Changes in protein expression during distinct stages of NK cell differentiation.

The average median S.D. and PEV reduction after applying different normalization methods compared with raw data. The average median S.D. and PEV reduction.

Occurrence of fur−-only genes and expected sensitivity to Fur.

Organelle proteomics in the cardiovascular system.Taylor et al.

Phosphopeptides identified harboring minimal binding motifs

MS3 for peptide identification and mapping phosphorylation sites

SCX chromatography at low pH permits strong enrichment of phosphopeptides of distinct solution charge states.A, the number of phosphopeptides (blue triangles)

Model of the change in receptor structure on engagement of the ligand IFN-γ. Model of the change in receptor structure on engagement of the ligand IFN-γ.

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Survey of phosphorylation motifs Survey of phosphorylation motifs.A, a query of the primary sequences surrounding the identified phosphorylation sites reveals potential links to distinct kinase activities. Survey of phosphorylation motifs.A, a query of the primary sequences surrounding the identified phosphorylation sites reveals potential links to distinct kinase activities. In addition to proline-directed phosphorylation events, strings of acidic residues (primarily downstream) of the phosphorylation site (B) or basic residues (primarily upstream) of the phosphorylation site (C) were prominent. Bryan A. Ballif et al. Mol Cell Proteomics 2004;3:1093-1101 © 2004 The American Society for Biochemistry and Molecular Biology