Computational protocol: Hyaluronic Acid Coated Chitosan Nanoparticles Reduced the Immunogenicity of the Formed Protein Corona

Similar protocols

Protocol publication

[…] Raw data files were subjected to the Proteome Discoverer software version 1.4 (Thermo Scientific) to set up the workflow, files were then submitted to Sequest by the Proteome Discoverer Daemon (Thermo Scientific). Peak lists in the range from 350–5000 m/z were searched against the Bovine.fasta (http://www.uniprot.org/). Carbamidomethylation of cysteine was set as a fixed modification, and oxidation of methionine was set as a variable modification. Peptide tolerance was allowed to be ±15 ppm; fragment mass tolerance was allowed to be ±0.8 Da, with a maximum of 2 missed cleavages. The Percolator peptide confidence filter was set to “medium”. All Proteome Discoverer search parameters are provided in Supplementary Table  and all identified proteins are given in Supplementary Tables – For statistical analysis, a stringent criterion was applied to distinguish false protein identities from true ones within each formed protein coronas. True proteins need to be present in all experimental triplicates in order to be analyzed further. To gain further insight into the nature and characteristics of the identified proteins on each of the different nanoparticles, bioinformatics analysis using Gene-Ontology (GO) enrichment terms was carried out. The proteins identified from the nanoparticles through the 1D gel-Nano LC-Tandem Mass Spectrometry were then annotated based on their respective subcellular localization, molecular function, and biological processes using the Uniprot GO classification with minor modifications. The term “Inflammatory Response” is used to represent six GO terms combined (Immune process, defense response, immune process regulation, complement pathway, response to stimulus, and cell death). Supplementary Figure  was generated with after removing uncharacterized proteins. The inflammatory NP-protein-GO network map was generated based on four molecular functions (inflammatory response, coagulation, cell adhesion, and enzymatic inhibitors) after excluding the common proteins shared by all NPs in addition to excluding uncharacterized proteins. […]

Pipeline specifications