WBPaper00053289:DREAM-target

N.A. Transcripts with promoter regions binding DREAM protein complex, according to ChIP-seq of E2F-DP (DPL-1 and EFL-1) and MuvB (LIN-9, LIN-37, LIN-52, and LIN-54) of N2 late embryo.

WBPaper00038213:E.coli(LF82)_72h_upregulated

Raw data were converted into a single peak list file using the in-house-developed software DTASupercharge and searched against the C. elegans NCBI nonredundant database using MASCOT 2.0 (Matrix Science, London, UK) with the following parameters: carbamidomethylcysteine was set as fixed modification and methionine oxidation, deamidation of asparagine and glutamine, and protein amino-terminal acetylation were set as variable modifications. 15N Metabolic was chosen as quantification mode. Two miss cleavages were allowed; enzyme specificity was trypsin D/DP, precursor mass accuracy had to be within 30 ppm, and the fragment spectra mass accuracy was set at 0.8 Da. The identified peptides were recalibrated using MSQuant (version 1.4.3a89), results were combined using MGF combiner (version 1.05) and re-searched using MASCOT 2.0 with the above mentioned parameters except that the precursor mass tolerance was set to 5 ppm. MSQuant and in-house-developed script N15-patch was used to quantify peptides and all spectra were manually verified. The represented protein ratio is calculated by averaging all peptide ratios for that protein. To correct for mixing errors, protein ratios were normalized by adjusting the median ratio to 1. To determine the number of false-positive peptide hits the data were searched against a decoy database and the MASCOT peptide score was adjusted to yield a number of false-positive peptide identifications of less than 1%. Only proteins identified by two or more unique peptides were considered. Two biological replicates were analyzed. Proteins whose abundance increased more than 1.5-fold, after 72 h of infection with bacteria LF82.

WBPaper00038213:E.coli(LF82)_24h_upregulated

Raw data were converted into a single peak list file using the in-house-developed software DTASupercharge and searched against the C. elegans NCBI nonredundant database using MASCOT 2.0 (Matrix Science, London, UK) with the following parameters: carbamidomethylcysteine was set as fixed modification and methionine oxidation, deamidation of asparagine and glutamine, and protein amino-terminal acetylation were set as variable modifications. 15N Metabolic was chosen as quantification mode. Two miss cleavages were allowed; enzyme specificity was trypsin D/DP, precursor mass accuracy had to be within 30 ppm, and the fragment spectra mass accuracy was set at 0.8 Da. The identified peptides were recalibrated using MSQuant (version 1.4.3a89), results were combined using MGF combiner (version 1.05) and re-searched using MASCOT 2.0 with the above mentioned parameters except that the precursor mass tolerance was set to 5 ppm. MSQuant and in-house-developed script N15-patch was used to quantify peptides and all spectra were manually verified. The represented protein ratio is calculated by averaging all peptide ratios for that protein. To correct for mixing errors, protein ratios were normalized by adjusting the median ratio to 1. To determine the number of false-positive peptide hits the data were searched against a decoy database and the MASCOT peptide score was adjusted to yield a number of false-positive peptide identifications of less than 1%. Only proteins identified by two or more unique peptides were considered. Two biological replicates were analyzed. Proteins whose abundance increased more than 1.5-fold, after 24 h of infection with bacteria LF82.

WBPaper00038213:E.coli(LF82)_72h_downregulated

Raw data were converted into a single peak list file using the in-house-developed software DTASupercharge and searched against the C. elegans NCBI nonredundant database using MASCOT 2.0 (Matrix Science, London, UK) with the following parameters: carbamidomethylcysteine was set as fixed modification and methionine oxidation, deamidation of asparagine and glutamine, and protein amino-terminal acetylation were set as variable modifications. 15N Metabolic was chosen as quantification mode. Two miss cleavages were allowed; enzyme specificity was trypsin D/DP, precursor mass accuracy had to be within 30 ppm, and the fragment spectra mass accuracy was set at 0.8 Da. The identified peptides were recalibrated using MSQuant (version 1.4.3a89), results were combined using MGF combiner (version 1.05) and re-searched using MASCOT 2.0 with the above mentioned parameters except that the precursor mass tolerance was set to 5 ppm. MSQuant and in-house-developed script N15-patch was used to quantify peptides and all spectra were manually verified. The represented protein ratio is calculated by averaging all peptide ratios for that protein. To correct for mixing errors, protein ratios were normalized by adjusting the median ratio to 1. To determine the number of false-positive peptide hits the data were searched against a decoy database and the MASCOT peptide score was adjusted to yield a number of false-positive peptide identifications of less than 1%. Only proteins identified by two or more unique peptides were considered. Two biological replicates were analyzed. Proteins whose abundance decreased more than 1.5-fold, after 72 h of infection with bacteria LF82.

WBPaper00038213:E.coli(LF82)_24h_downregulated

Raw data were converted into a single peak list file using the in-house-developed software DTASupercharge and searched against the C. elegans NCBI nonredundant database using MASCOT 2.0 (Matrix Science, London, UK) with the following parameters: carbamidomethylcysteine was set as fixed modification and methionine oxidation, deamidation of asparagine and glutamine, and protein amino-terminal acetylation were set as variable modifications. 15N Metabolic was chosen as quantification mode. Two miss cleavages were allowed; enzyme specificity was trypsin D/DP, precursor mass accuracy had to be within 30 ppm, and the fragment spectra mass accuracy was set at 0.8 Da. The identified peptides were recalibrated using MSQuant (version 1.4.3a89), results were combined using MGF combiner (version 1.05) and re-searched using MASCOT 2.0 with the above mentioned parameters except that the precursor mass tolerance was set to 5 ppm. MSQuant and in-house-developed script N15-patch was used to quantify peptides and all spectra were manually verified. The represented protein ratio is calculated by averaging all peptide ratios for that protein. To correct for mixing errors, protein ratios were normalized by adjusting the median ratio to 1. To determine the number of false-positive peptide hits the data were searched against a decoy database and the MASCOT peptide score was adjusted to yield a number of false-positive peptide identifications of less than 1%. Only proteins identified by two or more unique peptides were considered. Two biological replicates were analyzed. Proteins whose abundance decreased more than 1.5-fold, after 24 h of infection with bacteria LF82.