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

Slides:

Advertisements

Similar presentations

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

Advertisements

Sequence alignment of C-terminal phosphorylated plant aquaporins

Principle for quantification of phosphorylation of the C-terminal tail of AtPIP2;1. Principle for quantification of phosphorylation of the C-terminal tail.

MALDI-TOF MS spectrum of phosphopeptides from plant PM 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

Experimental overview A sequential protein and peptide IMAC enrichment was analyzed by four different LC-MS/MS strategies. Experimental overview A sequential.

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

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,

Complementary identification and novel protein discovery

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.

Work flow for the LAXIC strategy to quantify the phosphorylation change in response to osmotic stress. Work flow for the LAXIC strategy to quantify the.

Top-down protein identification.

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

Schematic representation of proteogenomic annotation strategy.

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

Global visualization of antigen and epitope discovery.

Relative abundance of proteins identified in MALDI IMS

Representative example of LAXIC performance for complex plant phosphoproteome. Representative example of LAXIC performance for complex plant phosphoproteome.A.

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.

NanoLC-MS/MS/based analysis of proteome differences between colonospheres and isogenic differentiated tumor cells. NanoLC-MS/MS/based analysis of proteome.

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

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.

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

MRNAs that show increased protein synthesis following UPF1 depletion are enriched for those with very long 3′UTRs. mRNAs that show increased protein synthesis.

High correlation of expression changes of NMD-regulated genes identified by both the pSILAC screen and previously reported global RNA screens after UPF1.

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.

Analysis of newly synthesized proteins by combined pulsed SILAC and click chemistry enrichment. Analysis of newly synthesized proteins by combined pulsed.

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

Putative targets of miRNAs directly induced by p53 with down-regulated mRNA- and de novo protein synthesis or reduced de novo protein synthesis only. Putative.

Interaction networks of the regulated phosphoproteins.

LC-MS/MS analyses of synthetic peptides with SUMO1 and SUMO3 remnant chains using ETD, CID, and HCD activation modes. LC-MS/MS analyses of synthetic peptides.

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.

A, Absolute ion intensities of m/z 322, 922 and 1522 as function of the transfer time. A, Absolute ion intensities of m/z 322, 922 and 1522 as function.

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.

Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a as compared with the strain MW001. Transcriptionally regulated genes in Δsaci_ptp and Δsaci_pp2a.

Bar plot representation of the transcriptomic changes in Δsaci_ptp and Δsaci_pp2a. Bar plot representation of the transcriptomic changes in Δsaci_ptp and.

Biochemical characterization of the protein phosphatases Saci-PP2A.

Biochemical characterization of the protein phosphatases Saci-PTP.

Illustration of chromatography metric C-2A applied to LC-MS/MS data from three Thermo LTQ systems in analyses of yeast proteome samples in CPTAC Study.

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.

2-D gel images visualized by Coomassie Brilliant Blue staining representing total proteins extracted from HCT-8 under apoptotic conditions in 2 mm Gln.

Overlap between changes in de novo protein synthesis after p53- or miR-34a-induction. Overlap between changes in de novo protein synthesis after p53- or.

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.

Peptide mass spectra of SUMO target proteins.

Phosphopeptides identified harboring minimal binding motifs

Survey of phosphorylation 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)

Presentation transcript:

Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. The IPI Arabidopsis protein database was used as the background database to normalize the score against random peptide sequences. Motifs 1, SnRK2 kinase family motif; Motif 2, CKII motif; Motif 3 and 4, unknown phosphorylation motifs. Liang Xue et al. Mol Cell Proteomics 2013;12:2354-2369 © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.