PMC:7443692 / 70538-72116 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7443692","sourcedb":"PMC","sourceid":"7443692","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7443692","text":"Quantification and Statistical Analysis\nRaw glycoproteomic data from the mass spectrometers was searched using Proteome Discoverer v1.4 (SEQUEST), Protein Metrics Inc. Byonic v3.8.13, and pGlyco v2.2.2. For data searches using Proteome Discoverer, the results were processed to apply false discovery rate filtering using ProteoIQ v2.7. For the deglycosylated protein work, search results from SEQUEST were filtered in ProteoIQ with a 1% false discovery rate at the protein level and 10% at the peptide level. For N-linked glycopeptide analysis, pGlyco was used with false discovery rate of 1% at the glycan level and 10% at the peptide level. For disulfide bond analysis and O-glycopeptide searches, Byonic was used and the false discovery rate was set to 1%. All mass spectrometry results were manually curated.\nAntigen accessibility simulations were carried out as described in the Method Details section and the mean of four simulations (three of length 350ns, one of length 200ns; amounting to 1.25 μs of total molecular dynamics simulation time) were utilized. Glycan-glycan and glycan-peptide interactions were also calculated based on simulations as a percentage of time residues were in contact and averaged (mean) to produce the corresponding supplemental (colored) sequence figures with the raw numbers for coloring present also in each corresponding supplemental table tab. 3D distances were computed using Rpdb as described in more detail in the Method Details section. This data is presented using box \u0026 whisker plots with all underlying statistics calculated in 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