Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Tchitchek, Nicolas; Eisfeld, Amie J; Tisoncik-Go, Jennifer; Josset, Laurence; Gralinski, Lisa E; Bécavin, Christophe; Tilton, Susan C; Webb-Robertson, Bobbie-Jo; Ferris, Martin T; Totura, Allison L; Li, Chengjun; Neumann, Gabriele; Metz, Thomas O; Smith, Richard D; Waters, Katrina M; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G

Quantitative LC-MS datasets were processed using the PRISM Data Analysis system [59] , which is a series of software tools developed in-house (e.g. Decon2LS [60] and VIPER [61] ; freely available at http://ncrr.pnl.gov/ software/). Individual steps in this data processing approach are reviewed here [54] . The peptide identities for detected features in each dataset (i.e. a single LC-MS analysis) were determined for features matched to AMT tags with high confidence based upon the accurate measured monoisotopic masses and NETs for each of the 39,744 peptides in the filtered AMT tag database within initial search tolerances of ± 6 ppm and ± 0.025 NET for monoisotopic mass and elution time, respectively. The peptides identified from this matching process were retained as a matrix for subsequent data analysis. The raw quantitative proteomics data can be accessed at the PNNL Biological MS Data and Software Distribution Center (http://omics.pnl.gov/) in the Systems Virology Contract Data folder within the Browse Available Data folder.