MS-viewer: a web-based spectral viewer for proteomics results

Abstract

The sharing and viewing of peptide identification results from search engines analyzing mass-spectrometry-based proteomic data is made difficult by the range of analysis tools employed, in that each produces a different output format. Annotated results associated with a journal article often have to be made available, but providing these in a format that can be queried by other researchers is often difficult. This is because although standard formats for results have been developed, these are not necessarily easy to produce. In this manuscript we describe the MS-Viewer program, part of the Protein Prospector Web package, which uses easy-to-create tabular files as input for providing highly interactive viewing of search engine results. Thanks to the simplicity and flexibility of the input format, results from a wide variety of search engines have been successfully viewed through the Web interface of this tool.

Fig. 1.

Screenshot of the MS-Viewer submission page. At the top of the page is the link to previously submitted results, which can be viewed by inputting a search key for a particular dataset. Underneath are the fields for submitting new data. Users browse to select a peak list and results file. If they specify their results file format as Protein Prospector tab-delimited, Mascot csv, or X! Tandem tab-delimited text, then MS-Viewer is able to automatically recognize the columns it needs, whereas if ‘Other’ is selected the submitter must indicate in which columns required information is located. At the bottom of the page, users specify default parameters used for displaying and re-searching spectra.

Fig. 2.

Example of MS-Viewer displaying an annotated spectrum for a peptide in which the modification site localization was ambiguous. The peptide has two potential HexNAc modification site localizations shown in different colors; those peak assignments common to both are labeled in black, and those assignments unique to one or the other are labeled in the relevant color.