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Results: 6

1.
Fig. 5.

Fig. 5. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Identification repeatability—comparison of GPS and SCX. The reproducibility of the MS/MS identification was evaluated by determining the identification overlap for all replicate runs. A, percentage peptide ID overlap in replicate technical (capture + LC-MS/MS) and biological replicate GPS-assays (based on six CIMS antibodies) (biosample 1, ethanol (K6, R10) - glucose; biosample 2, ethanol - glucose (K6, R10)). It should be noted that the generated values were based on separate capture and LC-MS/MS steps. B, percentage peptide ID overlap for replicate runs (same SCX-fraction analyzed twice with LC-MS/MS) and biological replicate runs for the eight generated SCX fractions.

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.
2.
Fig. 4.

Fig. 4. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Quantitative data—comparison of GPS and SCX. SILAC-labeled yeast proteomes, cultivated in ethanol or glucose, were profiled using GPS (based on six CIMS antibodies) and SCX. The correlation between the data sets was examined. A, all identified peptides for biosample 1 (isotopic amino acids present in ethanol condition). B, normalized data for all identified peptides in biosample 1 (isotopic amino acids present in ethanol condition). C, all identified proteins for biosample 1 (isotopic amino acids present in ethanol condition). D, normalized data for all identified proteins in biosample 1 (isotopic amino acids present in ethanol condition).

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.
3.
Fig. 3.

Fig. 3. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Coverage—comparison of GPS and SCX. Yeast SILAC-proteomes, cultivated in ethanol or glucose, were profiled using GPS and SCX. A, Venn diagram showing the number of peptides identified by GPS (based on 6 CIMS antibodies) and SCX; a total number of 4126 peptides were identified of which 417 were detected in both. B, Venn diagram showing the number of proteins identified by GPS and SCX; a total number of 987 proteins were identified of which 382 were detected in both. C, Statistics of all the identified peptides and proteins. D, peptide length plotted for all identified peptides using GPS and SCX. E, peptide length plotted for peptides identified in both biological replicates with a ratio count of ≥2 using GPS and SCX.

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.
4.
Fig. 6.

Fig. 6. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Biological relevance of identified proteins for carbon and ethanol metabolism. The biological relevance of differentially expressed proteins in glucose versus ethanol yeast was evaluated. The GPS assay was based on six CIMS antibodies. A, all identified proteins by GPS for biosample 1 (ethanol (K6, R10) - glucose) plotted as overall fold change as a function of protein intensity in the MS. Protein ratios are color-coded according to their ratio significance (significance B, as described in (29)). B, all identified proteins by SCX for biosample 1(ethanol (K6, R10) - glucose) plotted as overall fold change as a function of protein intensity in the MS. Protein ratios are color-coded according to their ratio significance (significance B, as described in (29)). C, GPS and SCX analysis of the central carbon metabolism. Protein expression values generated by GPS and SCX were mapped to the central carbon metabolism pathway(s) displayed in a condensed version according to (34). D, Protein-protein interaction maps of GPS identified up- and down-regulated proteins for biosample 1. Thirty-one up-regulated proteins (limited to proteins reported/annotated with a single Swiss-Prot ID, MaxQuant significance B value of p < 0.05 resulting in proteins with ≥5.5-fold up-regulation). Twenty-three down-regulated proteins (limited to proteins reported/annotated with a single Swiss-Prot ID, MaxQuant significance B value of p < 0.1 resulting in proteins with ≥twofold down-regulation).

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.
5.
Fig. 2.

Fig. 2. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Dynamic range and sensitivity. Glucose grown yeast SILAC-proteomes, mixed at three ratios of H and L, were profiled using two CIMS antibodies, A, CIMS-17-E02 and B, CIMS-33–3D-F06, and mapped to the known protein abundances generated by orthogonal methods (32). In total, the data was based on six capture trials (two for each isotopically labeled spike in proteome ratio mix) per CIMS-antibody (supplemental Tables S3–S5). For Swiss-Prot ID's matching two different synonymous yeast SGD ids and two different values in (32), the highest reported value was plotted. In cases with multiple Swiss-Prot ID's, they were checked in alphabetical order for presence in (32), and if no value was present the second Swiss-Prot id was checked and onwards. A number of identified peptides/proteins were reported to be present in less than 50 copies/cell or had no reported value at all and thereby could not be plotted and are listed separately in a box.

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.
6.
Fig. 1.

Fig. 1. From: Quantitative Proteomics Targeting Classes of Motif-containing Peptides Using Immunoaffinity-based Mass Spectrometry.

Quantitative accuracy and reproducibility. A, Experimentally refined binding motif amino acid sequences as compiled from all MS-MS detected captured peptides (excluding background peptides) in the spike-in proteome experiments (glucose grown SILAC-labeled yeast proteomes mixed at three ratios of H and L) for two CIMS antibodies, clones CIMS17-E02 (97 peptides) and CIMS-33–3D-F06 (142 peptides). The frequency of each individual residue in the last six C-terminal positions is indicated. B, Peptide intensity/ratio distribution for peptides enriched, from predefined proteome mixtures, by the two CIMS antibodies. Data limited to YXR motif-containing peptides for CIMS-17-E02 and DXR motif-containing peptides for CIMS-33–3D-F06. (The two replicate captures for each condition were analyzed as one experiment in MaxQuant. Hence, raw (non-normalized) ratios, as calculated from associated redundant peptide ratios by means of median of the two replicates, are displayed. Furthermore, data limited to peptides with MaxQuant reported ratios in all conditions and replicate capture trials resulting in 39 different peptides for CIMS-17-E02 and 64 different peptides for CIMS-33–3D-F06). Noteworthy, the peptides were ordered based on total intensity, resulting in that peptide number 39 and 64 were the two peptides observed with the highest total intensity. C, The same data as in panel B, but now compensated (normalized) against the corresponding 50/50 ratio measurement set to be 0. D, Reproducibility between replicate capture experiments for CIMS-17-E02 (limited to YXR motif-containing peptides) and CIMS-33–3D-F06 (limited to DXR motif-containing peptides).

Niclas Olsson, et al. Mol Cell Proteomics. 2012 August;11(8):342-354.

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