Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. Comparison of.

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

NSAF and GeneChip data have similar distribution properties.

Sequence alignment of C-terminal phosphorylated plant aquaporins

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,

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

Plasma CEP adducts and autoantibodies by donor age.

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

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

Protein information in the Human Protein Atlas.

Two-dimensional electrophoresis results and validation with Western blotting. Two-dimensional electrophoresis results and validation with Western blotting.

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.

Epitope Mapping Performance using a single peptide microarray.

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

A, Averaged full MS (ions converted to monoisotopic MW by Xcalibur Xtract) of Segment I-3 (see supplemental Fig. A, Averaged full MS (ions converted to.

Bottom-up proteomic characterization of MALDI IMS samples.

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

Success rates in validation of antibodies from external providers

Results from the Morris water task.

Technical reproducibility and biological variability.

A, Base peak chromatogram of apomyoglobin digest generated by 0

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

A, myelinated nerve fibers in the control and biopsied mouse striatum were stained with anti-MBP antibody. A, myelinated nerve fibers in the control and.

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.

A, schematic presentation of fetuin-A domains.

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.

Protein microarrays for validation of antibodies.

Cleavage and splicing in a representative specific substrate sequence by yeast active site β subunits. Cleavage and splicing in a representative specific.

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.

Manual assessment of the quality of peptide spectra with scores ranging from 5 to 10 of OFFGEL electrophoresis fractions 3 and 4 that were rejected by.

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

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

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.

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.

Examples of protein that display profiles corresponding to GO/GROW and STOP signals.A, example of STOP profile: normalized spot volume profile of apoA-I.

K-Means clustering of protein and mRNA expression patterns after PPAR agonists treatments. k-Means clustering of protein and mRNA expression patterns after.

Number of genes/antibodies included in the database.

The principle of the immuno-SILAC method.

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

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

A and B, ROC curves of the proteomics panel diagnosis.

Summary of intralaboratory and interlaboratory variation for metrics for three LTQ and three LTQ-Orbitrap instruments in six replicate analyses of a tryptic.

Stability and variation of metrics over a range of sample injection amounts. Stability and variation of metrics over a range of sample injection amounts.

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.

Proteomic analysis of invasive TCCs

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.

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

Schematic of AIMS-to-MRM experiment.

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.

Comparison of fluorescence spectra of cells expressing the FL-IFN-γR2/EBFP and FL-IFN-γR2/GFP chains in the presence and absence of the IFN-γR1 chain and.

MS3 for peptide identification and mapping phosphorylation sites

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.

Presentation transcript:

Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. The upper part of each panel shows the binding intensities in median fluorescence intensity to overlapping 12-mer peptides in the epitope mapping, where epitopes are shown as clusters of bound peptides. The blue horizontal bars in the lower part show the locations of peptides identified in immuno-SILAC screening on their corresponding antigen, and gray vertical lines indicate trypsin cleavage sites. Fredrik Edfors et al. Mol Cell Proteomics 2014;13:1611-1624 © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.