Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum

Patton, John B.; Bennuru, Sasisekhar; Eberhard, Mark L.; Hess, Jessica A.; Torigian, April; Lustigman, Sara; Nutman, Thomas B.; Abraham, David

Mass spectrometer RAW data files were converted to mzML format using msconvert [51] . MGF files were generated from mzML using the Peak Picker HiRes tool, part of the OpenMS framework [52] . All searches were performed on Amazon Web Services-based cluster compute instances using the Proteome Cluster interface. Detailed search parameters are printed in the search output XML files. Briefly, all searches required 10 ppm precursor mass tolerance, 0.02 Da fragment mass tolerance, strict tryptic cleavage, up to 2 missed cleavages, fixed modification of cysteine alkylation, variable modification of methionine oxidation and protein-level expectation value scores of 0.0001 or lower. Proteome Cluster builds species-and genus-specific protein sequence libraries from the most current UniProtKB distribution [53] . MGF files were searched using the most recent protein sequence libraries available from UniProtKB using X!Tandem [54] and OMSSA [55] . XML output files were parsed and non-redundant protein sets determined using Proteome Cluster based on previously published rules [56] . MS1-based isotopoic features were detected and peptide peak areas were calculated using the FeatureFinderCentroid tool, part of the OpenMS framework [52] . Proteins were required to have 1 or more unique peptides across the analyzed samples with E-value scores of 0.0001 or less.