WBPaper00005943:L4_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. L4 specific.

WBPaper00005943:L1-L2_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. L1 and L2 specific.

WBPaper00005943:adult_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. Adult specific.

WBPaper00005943:L1_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. L1 specific.

WBPaper00005943:L4-adult_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. L4 and adult specific.

WBPaper00005943:L3_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified. Life stage specific marker proteins according to proteomic analysis. L3 specific.

WBPaper00006047:25C_temperature_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cystein residues set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 5070 ppm mass accuracy and maximally 1 or 2 miscleavage sites were met with a significant probability score (usually above 100) and nearly all dominant signals of the spectrum were assigned to the protein or mixture of proteins identified. Proteins expressed significantly higher in N2 animals growing at 25 centigrade comparing to at 15 centigrade, according to proteomic study.

WBPaper00006047:15C_temperature_specific

Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cystein residues set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 5070 ppm mass accuracy and maximally 1 or 2 miscleavage sites were met with a significant probability score (usually above 100) and nearly all dominant signals of the spectrum were assigned to the protein or mixture of proteins identified. Proteins expressed significantly higher in N2 animals growing at 15 centigrade comparing to at 25 centigrade, according to proteomic study.

WBPaper00028360:Phospho-Sulfo-Modified_proteins

The protein identification was performed by PMF analysis with the spectra in the positive ion mode. Database searches against all entries of Refseq Release 13 were carried out using Biotools 2.2 (Bruker Daltonics) and MASCOT search engine (Matrix Science, London, UK). The search parameters allowed carbamidomethylation of Cys, partial oxidation of Met, 150 ppm for mass tolerance, and one missed cleavage per peptide. The protein identification results were accepted in consideration of the MASCOT score. Furthermore, the reliability of the results was confirmed by the additional information of the spectrum observed in the negative ion mode. Phosphorylation and sulfonation peptides were detected by Mass Spectrometry using the positive and negative ion modes with mono-ammonium phosphate as the matrix additive.

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.