MassSieve: panning MS/MS peptide data for proteins

Abstract

We present MassSieve, a Java-based platform for visualization and parsimony analysis of single and comparative LC-MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment algorithms has led to the need for a tool to merge and evaluate the increasing data set sizes that result from LC-MS/MS-based shotgun proteomic experiments. MassSieve supports reports from multiple search engines with differing search characteristics, which can increase peptide sequence coverage and/or identify conflicting or ambiguous spectral assignments.

Figure 1

The MassSieve pipeline filters for processing peptide identifications into protein identifications.

Figure 2

Main window of MassSieve. All display areas are moveable and all columns are sortable and moveable. The tree on the left expands to show peptide and protein lists and parsimony hierarchy. Selection of a specific peptide or protein triggers an update of related information in corresponding windows. Information can be shown for total experiment and individual protein. Upper most tabs denote individual experiments or groups, with each experiment containing culled results for each group and corresponding parsimonious protein lists.