Mason Example Applicaton: Protein Sequence Coverage
A single Mason viewer may contain multiple rows. The Mason viewer below depicts the sequence coverage for a given protein from seven mass spectrometry proteomics experiments. Each row is an experiment and the red regions indicate where the identified
peptides in each experiment map to the protein sequence. (The top row is the combination of the lower seven rows.) The shading indicates the statistical significance of those identifications, where
light red indicates weaker evidence. The bars to the right of the row indicate the total sequence coverage for the protein in each experiment. Each peptide may be moused-over to reveal
statistics associated with the identification. The red box with a plus-sign (+) may be clicked to expand that row to reveal overlapping peptides.
This example also illustrates how vertical lines may be defined to illustrate distinct positions of interest in the sequence that are
relevant for the data being displayed. In this example. clicking the checkbox below will illustrate the locations in the protein sequence expected
to be cut by the trypsin protease, which was used to digest the proteins in the experiment before peptides were analyzed by the mass spectrometer.
Show/hide trypsin cut points
Unable to show Mason Viewer due to lack of SVG support in this browser
Please use a different browser to view the Mason Viewer.
Possible choices are Firefox, Google Chrome, Internet Explorer version 9 or higher.
Below is an example of how the data used to generate the viewer above are formatted as a JavaScript object. Of particular note is the
rowItems array of objects defining the data for each row. Each of these has a rowData object, which
may contain any arbitrary data to be used by callback functions. Each row also contains a blockItems array of objects
that defines the start and end position of each annotation, as well as a blockData object, which contains arbitrary
data to pass into callback functions for coloring, tooltips, and click behavior. Also note the vertLinesAllRowsItems, which
defines the vertical line positions when toggling vertical lines on and off. (A position of 3.5 defines a line between positions 3 and 4.)
var multiRowAllFeaturesMasonViewerData
=
// Data in the objects surrounding the object that holds the Mason Viewer data.
// This data is used for post AJAX processing and in the viewer creator and in call backs
{"status":"success",
"results":
{"proteinId":528817,"peptideCoverageAcrossAllRuns":64.200,
"protViewerCoreInputData":
// Input data to core Mason viewer starts here
{"maxSequenceLength":324,"rowItems":
[
// Data for the first row
{"label":"Run: 803",
// Blocks for this row
"blockItems":
[
/// Blocks for this row
{"blockData":{"id":4907595,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":6,"uniquePeptide":"Y"},
"startPos":18,"endPos":30},
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":5,"uniquePeptide":"Y"},
"startPos":56,"endPos":74},
{"blockData":{"id":19711760,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":4,"uniquePeptide":"Y"},"startPos":188,"endPos":207},
{"blockData":{"id":19713832,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":2,"uniquePeptide":"Y"},"startPos":115,"endPos":123},
{"blockData":{"id":16418191,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":177,"endPos":187},
{"blockData":{"id":18906090,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":31,"endPos":55},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55},
{"blockData":{"id":19713179,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":75,"endPos":95},
{"blockData":{"id":19713905,"peptideRunQValue":0.0020000,"peptideRunQValueDisplay":"2E-3","bestQValue":0.0010,"bestQValueDisplay":"1E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":235,"endPos":245},
{"blockData":{"id":19712499,"peptideRunQValue":0.0030000,"peptideRunQValueDisplay":"3E-3","bestQValue":0.0020,"bestQValueDisplay":"2E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":213,"endPos":224},
{"blockData":{"id":5093293,"peptideRunQValue":0.0030000,"peptideRunQValueDisplay":"3E-3","bestQValue":0.0020,"bestQValueDisplay":"2E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":232,"endPos":245},
{"blockData":{"id":19715811,"peptideRunQValue":0.0040000,"peptideRunQValueDisplay":"4E-3","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":3,"uniquePeptide":"Y"},"startPos":312,"endPos":324},
{"blockData":{"id":19716595,"peptideRunQValue":0.0040000,"peptideRunQValueDisplay":"4E-3","bestQValue":0.0020,"bestQValueDisplay":"2E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":308,"endPos":324},
{"blockData":{"id":5883099,"peptideRunQValue":0.0090000,"peptideRunQValueDisplay":"9E-3","bestQValue":0.0070,"bestQValueDisplay":"7E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":273,"endPos":307}
],
// additional data for this specific viewer, used by the call backs at the row level
"rowData":{"runId":803,"sequenceCoverage":60.500}
}, // End of data for the first row
// Start of the data for the second row
{"label":"Run: 811",
"blockItems":[
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":4,"uniquePeptide":"Y"},"startPos":56,"endPos":74},
{"blockData":{"id":19711760,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":3,"uniquePeptide":"Y"},"startPos":188,"endPos":207},
{"blockData":{"id":19713832,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":115,"endPos":123},
{"blockData":{"id":19714125,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":59,"endPos":74},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55},
{"blockData":{"id":16418191,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":177,"endPos":187},
{"blockData":{"id":19713836,"peptideRunQValue":0.0010000,"peptideRunQValueDisplay":"1E-3","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":2,"uniquePeptide":"Y"},"startPos":256,"endPos":266},
{"blockData":{"id":19715811,"peptideRunQValue":0.0010000,"peptideRunQValueDisplay":"1E-3","bestQValue":0.0010,"bestQValueDisplay":"1E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":312,"endPos":324},
{"blockData":{"id":19712499,"peptideRunQValue":0.0060000,"peptideRunQValueDisplay":"6E-3","bestQValue":0.0050,"bestQValueDisplay":"5E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":213,"endPos":224}
],
"rowData":{"runId":811,"sequenceCoverage":34.900}},
// Start of the data for the next row
{"label":"Run: 867","blockItems":[
{"blockData":{"id":19712499,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0020,"bestQValueDisplay":"2E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":213,"endPos":224},
{"blockData":{"id":19713832,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":115,"endPos":123},
{"blockData":{"id":19713905,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0020,"bestQValueDisplay":"2E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":235,"endPos":245},
{"blockData":{"id":19716254,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":255,"endPos":266},
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":56,"endPos":74},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55}],
"rowData":{"runId":867,"sequenceCoverage":25.000}},
// Start of the data for the next row
{"label":"Run: 858","blockItems":[
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":56,"endPos":74},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55},
{"blockData":{"id":19713832,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":115,"endPos":123},
{"blockData":{"id":19713836,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":256,"endPos":266}],
"rowData":{"runId":858,"sequenceCoverage":17.600}},
// Start of the data for the next row
{"label":"Run: 848","blockItems":[
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":2,"uniquePeptide":"Y"},"startPos":56,"endPos":74},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55},
{"blockData":{"id":19965306,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":19,"endPos":30}],
"rowData":{"runId":848,"sequenceCoverage":15.100}},
// Start of the data for the next row
{"label":"Run: 851","blockItems":[
{"blockData":{"id":256849,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":56,"endPos":74},
{"blockData":{"id":2597403,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":38,"endPos":55}],
// Vertical lines for this row
"rowData":{"runId":851,"sequenceCoverage":11.400}},
// Start of the data for the next row
{"label":"Run: 806","blockItems":[
{"blockData":{"id":19713832,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0000,"bestQValueDisplay":"0","totalPsm":1,"uniquePeptide":"Y"},"startPos":115,"endPos":123},
{"blockData":{"id":19716254,"peptideRunQValue":0E-7,"peptideRunQValueDisplay":"0","bestQValue":0.0010,"bestQValueDisplay":"1E-3","totalPsm":1,"uniquePeptide":"Y"},"startPos":255,"endPos":266}],
"rowData":{"runId":806,"sequenceCoverage":6.500}}
],
// Viewer wide data:
// Vertical lines data that will be displayed across all the rows.
// If the same lines are needed for all the rows, this is the most efficient as they result in far fewer
// SVG elements in the viewer.
// All the line positions in this case are on the half (using ".5") so that they land
// specifically on the edges/boundaries between the blocks.
// The data under "vertLineData" is passed to the callback for determining the color, tool tip, and click handling
"vertLinesAllRowsItems":
[
{"linePos":3.5,"vertLineData":{"type":"CP"}},
{"linePos":6.5,"vertLineData":{"type":"CP"}},
{"linePos":10.5,"vertLineData":{"type":"CP"}},
{"linePos":12.5,"vertLineData":{"type":"CP"}},
{"linePos":17.5,"vertLineData":{"type":"CP"}},
{"linePos":18.5,"vertLineData":{"type":"CP"}},
{"linePos":30.5,"vertLineData":{"type":"CP"}},
{"linePos":37.5,"vertLineData":{"type":"CP"}},
{"linePos":55.5,"vertLineData":{"type":"CP"}},
{"linePos":74.5,"vertLineData":{"type":"CP"}},
{"linePos":95.5,"vertLineData":{"type":"CP"}},
{"linePos":106.5,"vertLineData":{"type":"CP"}},
{"linePos":114.5,"vertLineData":{"type":"CP"}},
{"linePos":123.5,"vertLineData":{"type":"CP"}},
{"linePos":156.5,"vertLineData":{"type":"CP"}},
{"linePos":160.5,"vertLineData":{"type":"CP"}},
{"linePos":167.5,"vertLineData":{"type":"CP"}},
{"linePos":168.5,"vertLineData":{"type":"CP"}},
{"linePos":172.5,"vertLineData":{"type":"CP"}},
{"linePos":176.5,"vertLineData":{"type":"CP"}},
{"linePos":187.5,"vertLineData":{"type":"CP"}},
{"linePos":190.5,"vertLineData":{"type":"CP"}},
{"linePos":207.5,"vertLineData":{"type":"CP"}},
{"linePos":212.5,"vertLineData":{"type":"CP"}},
{"linePos":213.5,"vertLineData":{"type":"CP"}},
{"linePos":224.5,"vertLineData":{"type":"CP"}},
{"linePos":231.5,"vertLineData":{"type":"CP"}},
{"linePos":234.5,"vertLineData":{"type":"CP"}},
{"linePos":245.5,"vertLineData":{"type":"CP"}},
{"linePos":249.5,"vertLineData":{"type":"CP"}},
{"linePos":251.5,"vertLineData":{"type":"CP"}},
{"linePos":254.5,"vertLineData":{"type":"CP"}},
{"linePos":255.5,"vertLineData":{"type":"CP"}},
{"linePos":266.5,"vertLineData":{"type":"CP"}},
{"linePos":271.5,"vertLineData":{"type":"CP"}},
{"linePos":272.5,"vertLineData":{"type":"CP"}},
{"linePos":284.5,"vertLineData":{"type":"CP"}},
{"linePos":307.5,"vertLineData":{"type":"CP"}},
{"linePos":308.5,"vertLineData":{"type":"CP"}},
{"linePos":311.5,"vertLineData":{"type":"CP"}}
]
} // End of data for the core Mason Viewer, end of data for property "protViewerCoreInputData"
} // End of data for property "results"
};