- WBPaper00061377:MYRF-1_interacting
The fil-tering criteria were: 1% FDR at both the peptide level and the protein level; precursor mass toler-ance, 20 ppm; fragment mass tolerance, 20 ppm; the peptide length, 6100 aa. To identify high-confidence candidate interacting proteins, The WD-Scores of proteins identified in each IP-MS sam-ple were calculated against the identification results of 71 unrelated IP-MS samples, according tothe formulas from the CompPASS tutorial.
Proteins interacting with GFP-MYRF-1.
- WBPaper00061377:PAN-1_interacting
The fil-tering criteria were: 1% FDR at both the peptide level and the protein level; precursor mass toler-ance, 20 ppm; fragment mass tolerance, 20 ppm; the peptide length, 6100 aa. To identify high-confidence candidate interacting proteins, The WD-Scores of proteins identified in each IP-MS sam-ple were calculated against the identification results of 71 unrelated IP-MS samples, according tothe formulas from the CompPASS tutorial.
Proteins interacting with GFP-PAN-1.
- WBPaper00061377:MYRF-2_interacting
The fil-tering criteria were: 1% FDR at both the peptide level and the protein level; precursor mass toler-ance, 20 ppm; fragment mass tolerance, 20 ppm; the peptide length, 6100 aa. To identify high-confidence candidate interacting proteins, The WD-Scores of proteins identified in each IP-MS sam-ple were calculated against the identification results of 71 unrelated IP-MS samples, according tothe formulas from the CompPASS tutorial.
Proteins interacting with GFP-MYRF-2.
- WBPaper00035314:acetic-acid_RF3_downregulated
Differentially expressed proteins were selected based on at least twofold protein-expression change between control and treated samples.
Proteins that showed decreased expression after treatment with 100 ppm RF3, 50ppm acetic acid or both.
- WBPaper00035314:acetic-acid_RF3_upregulated
Differentially expressed proteins were selected based on at least twofold protein-expression change between control and treated samples.
Proteins that showed increased expression after treatment with 100 ppm RF3, 50ppm acetic acid or both.
- WBPaper00041072:UTX-1_interacting_protein
MS mass tolerance was set to 10 ppm, while MS-MS tolerance was set to 0.6 Da. Peptide validation was performed using Percolator and peptide false discovery rate (FDR) was set to 0.01. For additional filtering, maximum peptide rank was set to 1 and minimum number of peptides per protein was set to 2. Protein grouping was performed, in order to avoid presence of different proteins identified by non-unique peptides.
Proteins that physically interact with UTX-1, according to immunoprecipitation of UTX-1-GFP and mass spectrometry.
- WBPaper00049595:P.aeruginosa_48h_upregulated
In the MASCOT search the proteins were searched against a mass tolerance of +/- 50and 100 ppm with one missed cleavage per peptide were allowed in all searches. Proteins with consistent hit against different mass tolerance, different databases and significant score >50 only were accepted.
Proteins that showed significantly increased expression after 48 hours of infection by Pseudomonas aeruginosa PAO1 strain, accroding to 2D-DIGE and mass spectrometry.
- WBPaper00024245:gst-5-binding_control
Database searches using the monoisotopic peptide masses were undertaken using the Protein Prospector V3.2.1 MS-Fit program . Peptide modifications allowed during the search were: carboxymethylation of cysteines, oxidation of methionines, acetylation of peptide N-terminus and modification of peptide N-terminal Glu to pyroGlu. The maximum number of missed cleavages was set to 1 and the mass tolerance was limited to either 20 or 50 ppm.
Proteins that physically interact with GST-5 in N2 control condition, according to proteomic study after affinity purification, 2D-electrophoresis.
- WBPaper00049595:P.aeruginosa_24h_upregulated
In the MASCOT search the proteins were searched against a mass tolerance of +/- 50and 100 ppm with one missed cleavage per peptide were allowed in all searches. Proteins with consistent hit against different mass tolerance, different databases and significant score >50 only were accepted.
Proteins that showed significantly increased expression after 24 hours of infection by Pseudomonas aeruginosa PAO1 strain, accroding to 2D-DIGE and mass spectrometry.