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• _3 wasQuotedFrom 18178582 provenance.
• _3 value "TABLE II Proteins identified to be significantly (p < 0.05) and up- or down-regulated at least 1.5-fold affected by IR in the wild type thymocyte samples.The MS/MS spectra were searched against a mouse database containing 46,892 protein entries built from the National Center for Biotechnology non-redundant (NCBInr) database (downloaded May 2006) using TurboSEQUEST in BioWorks version 3.2 (ThermoElectron). The search parameters included: precursor mass tolerance, ± 2 amu; fragment mass tolerance, ± 1 amu; up to two missed trypsin cleavages; a static modification of +227.13 on cysteine for the light ICAT reagent; a variable modification of +9 on cysteine for the heavy ICAT reagent; and a variable modification for methionine oxidation. The search results were processed and analyzed using the Trans-Proteomic Pipeline (TPP) (Institute for Systems Biology). SEQUEST results were validated using the PeptideProphet software, which calculates a probability for each peptide identification (19). Quantitation was performed using the ASAPRatio software, which uses extracted ion chromatograms for quantitation, and the peptides were assigned to proteins using ProteinProphet (20, 21). Based in part on the peptide probability and the Sequest Xcorr score, a protein identification probability was calculated using ProteinProphet; only protein identifications with a probability >0.9 were retained for further consideration. This cutoff results in a calculated false discovery rate of <1% as determined by ProteinProphet. All single peptide identifications were manually verified, and the quantifications were also manually checked. The ASAPRatio software uses a statistical method for identification of outliers and excludes them from quantification (20). Proteins for which constituent unique peptides exhibited significantly different ratios were excluded from further analysis. Peptides that matched to multiple members of a protein family were grouped as such by ProteinProphet and maintained as a protein family for analysis unless a peptide unique to a specific family member was observed; protein isoforms were maintained in the same way unless a peptide that uniquely identified the specific isoform was observed. Proteins that exist in the database under different names and/or accession numbers were grouped together for analysis. Proteins were classified as significantly IR-responsive if the p value calculated by the ASAPRatio software was less than 0.05. " provenance.