- 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: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.
- 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: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-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: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.
- 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.
- WBPaper00043951:insoluble_protein_day16_N2
All the spectra were searched against target/decoy database and MASCOT significance threshold was chosen to achieve a targeted false discovery rate of 1%. For this analysis, the mascot significance threshold was 0.01. The peptide identification was considered valid if its corresponding mascot score was equal to or less than the threshold.
Insoluble protein isolated from day 16 animals, according to liquid chromotography and mass spectrometry.
- WBPaper00061479:hda-1(ne4747)_upregulated
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.
Transcripts that showed significantly increased expression in hda-1[KKRR] in gonads dissected from 1-day old adult animals.