Current Approaches on Viral Infection: Proteomics and Functional Validations

Zheng, Jie; Tan, Boon Huan; Sugrue, Richard; Tang, Kai

er isotopic distribution analysis (Xu et al., 2006) . And high sensitivity and specificity of ProLuCID could be achieved compared to SEQUEST. In addition to these searching algorithms, there emerge several multi-functional proteomic pipelines which could incorporate statistical analysis and guarantee high confident searching results. Since different search engines have distinctive algorithms and sensitivities, some important low-abundant hits may be identified by only few software. To cope with this problem, one advantage of Scaffold proteomic pipeline is that peptides simultaneously identified by several different searching engines, e.g., Mascot, SEQUEST, TANDEM, etc, could be integrated into "a folder" by Peptide Prophet Algorithm, resulting in a list of combined peptide sequences. And a further statistical calculation and validation by Protein Prophet algorithm is processed with MS/MS data to generate protein identifications (Searle, 2010) . Similarly, TPP also supports the original data generated by Mascot, SEQUEST, TAN-DEM, etc. Peptide or protein identification is performed by peptide prophet or protein prophet algorithm, respectively. It also combines the advantages of statistical validations by iProphet tool and quantitative analysis by XPRESS, ASAPRatio, or Libra algorithm 3 http://www.thegpm.org/ (Deutsch et al., 2010) . Moreover, the Scripps Research Institute developed an integrated Proteomics Pipeline (IP2), which provides a simple and efficient platform for rapid identifications and quantifications to proteomic researchers 4 . It is compatible with both SEQUEST and ProluCID search engines for high resolution MS spectra analysis (Xu et al., 2006) . Subsequently, DTASelect set spectrum filtering parameters to ensure low false-positive rate and refine the confidence of protein output (Tabb et al., 2002; Cociorva and Yates, 2007) . Census is further incorporated into IP2 to enable large-scale quantitative analysis on isotopelabeled, e.g., N15, SILAC, and iTRAQ, or label-free samples (Park et al., 2008) . Some well-established PTMs, especially phosphopeptides, could also be specifically searched during the IP2 ProluCID analysis step, yielding potential highlights for further functional validations.