Selected proteins identified using the PROP analysis that were preferentially identified <i>before</i> H₂O₂ oxidation treatment of cells.

†<p>Leading number indicates the number of unique peptides for a particular protein that were observed while the number in parentheses indicates the total number of scans that were observed for that protein. All of the scans tabulated passed a 3% FDR filter cutoff. An “X” indicates that no scans were observed that passed the FDR filter. The replicate analysis of 6 independent biological samples for both the control and H₂O₂ treated cells are shown. Data referred to in the text combine the replicate analyses.</p>‡<p>The pValue represents the product of the best (i.e. smallest) eValue score observed for each <i>unique</i> peptide sequence for the given protein. This provides a relative measure of the overall confidence that the protein was in the sample (i.e. a true positive), with 0.00E+000 representing the highest confidence.</p

Potential Consensus Sequence for Oxidized Cysteine Residues.

<p>The sequence logo representation of the frequency of the amino acid residues surrounding the oxidized cysteine residues, located at position “0”, that were identified from the PROP proteomics procedure.</p

Selected peptides that were observed with a cysteine residue that had been biologically oxidized from proteins that were preferentially identified <i>before</i> H₂O₂ oxidation treatment of cells.

†<p>The total number of scans that were observed for that peptide. All of the scans tabulated passed a 3% FDR filter cutoff. The replicate analysis of 6 independent biological samples for both the control and H₂O₂ treated cells are shown. Data referred to in the text combine the replicate analyses.</p>‡<p>The eValue represents the best (i.e. smallest) OMSSA eValue score matched to the particular peptide sequence. This provides a relative measure of the overall confidence that the peptide was in the sample (i.e. a true positive), with 0.00E+000 representing the highest confidence.</p>*<p>Lower case “c” indicates location of carboxyamidomethyl derivatization(s).</p

PROP-proteomics procedure.

<p>Schematic diagram showing steps involved in the PROP-proteomics procedure that are described in detail in both <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032527#s2" target="_blank">Methods</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032527#s3" target="_blank">Results</a>.</p

Selected proteins identified using the PROP analysis on six replicate cell cultures treated or not with H₂O₂ that were preferentially identified <i>after</i> H₂O₂ oxidation treatment of cells.

†<p>Leading number indicates the number of unique peptides for a particular protein that were observed while the number in parentheses indicates the total number of scans that were observed for that protein; in other words, a protein indicated as 3(13) had three unique peptides identified a total of 13 times. All of the scans tabulated passed a 3% FDR filter cutoff. An “X” indicates that no scans were observed that passed the FDR filter. The replicate analysis of 6 independent biological samples for both the control and H₂O₂ treated cells are shown. Data referred to in the text combine the replicate analyses.</p>‡<p>The pValue represents the product of the best (i.e. smallest) eValue score observed for each <i>unique</i> peptide sequence for the given protein. This provides a relative measure of the overall confidence that the protein was in the sample (i.e. a true positive), with 0.00E+000 representing the highest confidence.</p

Gene ontology (GO) analysis of proteins that were preferentially identified <i>after</i> H₂O₂ oxidation treatment of cells.

†<p>The adjusted pValue assigned to the biological process by the WebGestalt GO analysis using the hypergeometric statistical test with a BH multiple test adjustment.</p

Selected peptides that were observed with a cysteine residue that had been biologically oxidized from proteins that were preferentially identified <i>after</i> H₂O₂ oxidation treatment of cells.

†<p>The total number of scans that were observed for that peptide. All of the scans tabulated passed a 3% FDR filter cutoff. The replicate analysis of 6 independent biological samples for both the control and H₂O₂ treated cells are shown. Data referred to in the text combine the replicate analyses.</p>‡<p>The eValue represents the best (i.e. smallest) OMSSA eValue score matched to the particular peptide sequence. This provides a relative measure of the overall confidence that the peptide was in the sample (i.e. a true positive), with 0.00E+000 representing the highest confidence.</p>*<p>Lower case “c” indicates location of carboxyamidomethyl derivatization(s).</p