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LC-MS/MS and automated protein library searching provide a high-throughput strategy for peptide sequence assignments for identification of qualitative differences in comparative shotgun proteomics. However, the rapid increase in size and depth of analysis requires advancement in the speed, scale and flexibility of tools available for parsimony level data analysis. MassSieve has been developed as a platform for parsimony analysis of large scale MS/MS experiments, both for single and comparative analysis.
MassSieve supports reports from multiple search engines with differing probability-based search characteristics which can increase peptide sequence coverage and/ or identify conflicting or ambiguous spectral assignments. Label-free relative quantitative information is also available by spectral hit counts per peptide and per protein. Graphical display of each set of related peptides and proteins as well as user defined treatment of indeterminate peptides provides for visualization of possible isoforms or conflicting database entries.