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PLUM Browser - Graphically view peptides identified in a mass spectrometry experiment PLUM Browser is designed to graphically view peptides identified in a mass spectrometry experiment by the position in the sequence of the protein they were derived from.PLUM Browser is also used to query for sets peptides by their amino acid composition and their relative positions to one another.Originally, the PLUM Browser was developed for BIMM 185, which is a senior-level bioinformatics tool construction class at UCSD.Here are some key features of "PLUM Browser":· Sorting: You can sort your peptides and proteins by single-clicking any title header in the peptide and protein table. Click it again to reverse the sort.· Copy layout to clipboard: Right click the browser box and select 'copy to clipboard' to get the HTML contents of the browser box· Delete datasets/subsets: In the Data --> Select screen, you can right click and select delete. Note that if you delete a dataset that a subset relies on, then it will not work anymore!· View last query text: The Query --> Info menu item to view the text of the most recent query request.Requirements:· Java 1.5 or laterKnown Issues:· On occasion, just after you import some data, the peptide table column header text shifts to the left while the program remains open. If you don't perform the import first, this shift does not to occur.· There is very limited support for multiple datasets containing the same gene names and same peptides. There is logic that will properly display the peptides in the browser, but there is not proper support for querying or flagging multiple peptides. So, users are advised not to use this software to compare multiple runs of the same proteome (that is, having the same set of gene names).

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