Epitope Mapping Performance using a single peptide microarray.

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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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NSAF and GeneChip data have similar distribution properties.

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

NSAF and GeneChip datasets have similar PLGEM parameters.

PLGEM fits equally well on NSAF and GeneChip datasets

Enrichment of sequence disorder in the cytosolic phosphoproteome.

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,

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

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

Schematic of cellular role categories of theoretical (open bars) and identified proteins on a 2-D electrophoresis gel, pH 4–7 (black bars), in L. casei.

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.

Top-down protein identification.

Schematic of MS1 filtering.

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.

Schematic representation of proteogenomic annotation strategy.

Global visualization of antigen and epitope discovery.

The summary page for cancer profiles.

Relative abundance of proteins identified in MALDI IMS

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.

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.

Genome-wide analysis of p53 occupancy.

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

Technical reproducibility and biological variability.

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,

Cluster analysis and pathway-based characterization of differentially expressed genes and proteins from integrated proteomics. Cluster analysis and pathway-based.

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.

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.

Sequence similarity clusters of SET domain methyltransferases.

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.

Protein microarrays for validation of antibodies.

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

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.

2D-LC-MS/MS analysis of tryptic digest of HEK293-SUMO3 cells (2 μg inj

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

Example of MS/MS spectrum of peptide FPTLTGFNR (hypothetical protein with signal peptide EAK88888; N77) from a protein digestion mixture prepared by labeling.

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.

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

Serum LAMC2 levels in pancreatic adenocarcinoma (PDAC) and other samples from Japan. Serum LAMC2 levels in pancreatic adenocarcinoma (PDAC) and other samples.

Localization of selected clones in mammalian COS-7 cells.

Analytical metrics of yeast proteome analysis using the Q-OT-qIT (Fusion) as compared with qIT-OT (Orbitrap Elite) and Q-OT (Q-Exactive) hybrids. Analytical.

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

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.

Label-free pyQms quantification of metabolites and peptides.

GeneGoTM-based signaling pathway annotations of proteins identified in CD56+ NK cell subsets. GeneGoTM-based signaling pathway annotations of proteins.

Statistical evaluation of CD56+ NK cell subset data.

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.

Differential protein, mRNA, lncRNA and miRNA regulation by p53.

RNA expression data. RNA expression data. Heat maps comparing the normalized log2 of the ratios of Fur−, F90, and F1 signals on the cl20 control signal.

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

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Epitope Mapping Performance using a single peptide microarray. Epitope Mapping Performance using a single peptide microarray.A, Protein Antigenicity profiles of three validated T. cruzi antigens: CA-2/B13, 60 S Ribosomal protein P2 and Ribosomal Protein L19. Horizontal axes show the amino acid positions of the protein sequences; vertical axes show the smoothed and normalized mean intensity values from a single peptide chip (sera pool C, replicate 1). In magenta: signal from negative sample (N). In black: cumulative signal from the negative and positive sample (NP). In green: Chagas-specific signal (subtraction of NP-N). Blue marks near the baseline show the position of known B-cell epitopes (antigenic regions within these antigens), as reported in the literature. B, Density plots showing the distribution of area under the ROC curve (AUC) values, where AUC = 1 means perfect residue by residue correspondence of signal with localization of previous known epitopes for 9 validation antigens. Color code for samples is the same as for panel A. Magenta: AUCs centered on 0.5, meaning no predictive performance. Black: average AUC = 0.861, for cumulative negative + positive signal. Green: AUC = 0.96, corresponding to Chagas-specific signal (for the single best performing assay). Santiago J. Carmona et al. Mol Cell Proteomics 2015;14:1871-1884 © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.